GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Klebsiella michiganensis M5al

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1

Query= BRENDA::P25516
         (891 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS11940 BWI76_RS11940 aconitate
           hydratase 1
          Length = 890

 Score = 1611 bits (4171), Expect = 0.0
 Identities = 796/890 (89%), Positives = 835/890 (93%)

Query: 1   MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDITRLPKSLKVLLENLLRWQDGNSVTE 60
           MSSTLR ASKDTLQ KDKT+HYYSLPLAAK LGD++RLPKSLKVLLENLLRWQDG+SVT 
Sbjct: 1   MSSTLRAASKDTLQVKDKTWHYYSLPLAAKQLGDLSRLPKSLKVLLENLLRWQDGDSVTA 60

Query: 61  EDIHALAGWLKNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120
           EDIHALAGWLK+AHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL
Sbjct: 61  EDIHALAGWLKHAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120

Query: 121 SPVDLVIDHSVTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGIC 180
           SPVDLVIDHSVTVDRFGDD+AFEENVRLEMERNHERYVFL+WG+QAFSRFSVVPPGTGIC
Sbjct: 121 SPVDLVIDHSVTVDRFGDDDAFEENVRLEMERNHERYVFLRWGQQAFSRFSVVPPGTGIC 180

Query: 181 HQVNLEYLGKAVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
           HQVNLEYLG+AVWSE Q+GEW+A+PDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 181 HQVNLEYLGRAVWSEQQNGEWVAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240

Query: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300
           PVSMLIPDVVGFKL+GKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR
Sbjct: 241 PVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300

Query: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWRNPGDEPIFT 360
           ATIANMSPEYGATCGFFPIDAVTLDYMRL+GRSE+QV LVE YAKAQGMWR PGDEP+FT
Sbjct: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLTGRSEEQVALVEAYAKAQGMWRQPGDEPVFT 360

Query: 361 STLELDMNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQY 420
           STL LDM  VEASLAGPKRPQDRVAL DVP+AFAAS+ELEVN   KD++P+DY +NG QY
Sbjct: 361 STLALDMGTVEASLAGPKRPQDRVALGDVPQAFAASSELEVNHAQKDKRPIDYTLNGQQY 420

Query: 421 QLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYL 480
            LPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAV  GLK QPWVKASLAPGSKVVSDYL
Sbjct: 421 SLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVERGLKPQPWVKASLAPGSKVVSDYL 480

Query: 481 AKAKLTPYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRI 540
           A AKLTP+LDELGFNLVGYGCTTCIGNSGPLPDPIE AIK+ DLTVGAVLSGNRNFEGRI
Sbjct: 481 AHAKLTPWLDELGFNLVGYGCTTCIGNSGPLPDPIERAIKQGDLTVGAVLSGNRNFEGRI 540

Query: 541 HPLVKTNWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQ 600
           HPLVKTNWLASPPLVVAYALAGNMN++L  EP+G  + G PVYLKDIWPS  E+A+AVEQ
Sbjct: 541 HPLVKTNWLASPPLVVAYALAGNMNLDLTREPLGTGKDGQPVYLKDIWPSGIEVAQAVEQ 600

Query: 601 VSTEMFRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPAPVEDIH 660
           VSTEMFRKEYAEVFEGTAEWK I V RSDTY WQ DSTYIRLSPFFDEM   P PVEDIH
Sbjct: 601 VSTEMFRKEYAEVFEGTAEWKAIKVDRSDTYDWQNDSTYIRLSPFFDEMGVEPKPVEDIH 660

Query: 661 GARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGT 720
           GARILAMLGDSVTTDHISPAGSIK DSPAGRYLQ  GVER DFNSYGSRRGNHEVMMRGT
Sbjct: 661 GARILAMLGDSVTTDHISPAGSIKADSPAGRYLQNHGVERIDFNSYGSRRGNHEVMMRGT 720

Query: 721 FANIRIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDW 780
           FANIRIRNEMVPGVEGGMTRHLPD+  ++IYDAAM YK+E TPLAVIAGKEYGSGSSRDW
Sbjct: 721 FANIRIRNEMVPGVEGGMTRHLPDTQPIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDW 780

Query: 781 AAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN 840
           AAKGPRLLG+RVVIAESFERIHRSNLIGMGILPLEFPQG+TRKTLGL GEE+IDI +LQ 
Sbjct: 781 AAKGPRLLGVRVVIAESFERIHRSNLIGMGILPLEFPQGMTRKTLGLNGEERIDISNLQA 840

Query: 841 LQPGATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNML 890
           LQPG TVPVTLTRADG QEV+ CRCRIDTATELTYYQNDGILHYVIRNML
Sbjct: 841 LQPGMTVPVTLTRADGRQEVIDCRCRIDTATELTYYQNDGILHYVIRNML 890


Lambda     K      H
   0.317    0.135    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2481
Number of extensions: 100
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 891
Length of database: 890
Length adjustment: 43
Effective length of query: 848
Effective length of database: 847
Effective search space:   718256
Effective search space used:   718256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)

Align candidate BWI76_RS11940 BWI76_RS11940 (aconitate hydratase 1)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01341.hmm
# target sequence database:        /tmp/gapView.5251.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01341  [M=876]
Accession:   TIGR01341
Description: aconitase_1: aconitate hydratase 1
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
          0 1523.2   0.0          0 1523.0   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS11940  BWI76_RS11940 aconitate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11940  BWI76_RS11940 aconitate hydratase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1523.0   0.0         0         0       1     876 []      18     890 .]      18     890 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1523.0 bits;  conditional E-value: 0
                               TIGR01341   1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvl 71 
                                             k+ +yysl+ ++++l+++s+lpksl++lle++lr++dg +++ ed++al+ w k++++d+eia++parv++
  lcl|FitnessBrowser__Koxy:BWI76_RS11940  18 KTWHYYSLPLAAKQLGDLSRLPKSLKVLLENLLRWQDGDSVTAEDIHALAGWLKHAHADREIAYRPARVLM 88 
                                             578******************************************************************** PP

                               TIGR01341  72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykf 142
                                             qdftGvpavvdlaa+reavk+lg+d++k+npl+pvdlvidhsv+vd++g+++a+e+nv+le+ern+ery f
  lcl|FitnessBrowser__Koxy:BWI76_RS11940  89 QDFTGVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHSVTVDRFGDDDAFEENVRLEMERNHERYVF 159
                                             *********************************************************************** PP

                               TIGR01341 143 lkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGG 213
                                             l+w+++af++++vvppgtGi+hqvnleyl+++v++++++ge++a+pd+lvGtdshttminGlGvlGwGvGG
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 160 LRWGQQAFSRFSVVPPGTGICHQVNLEYLGRAVWSEQQNGEWVAFPDTLVGTDSHTTMINGLGVLGWGVGG 230
                                             *********************************************************************** PP

                               TIGR01341 214 ieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladra 284
                                             ieaeaa+lGqpvs+ +p+v+G+kl GklreG+tatdlvltvt++lrk+gvvgkfvef+G+gl++l+ladra
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 231 IEAEAAMLGQPVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRA 301
                                             *********************************************************************** PP

                               TIGR01341 285 tianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdvea 355
                                             tianm+peyGat++ffpid+vtl+y+rltgr+e++v lve+y+kaq+++++ ++ep++t+++ ld+ +vea
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 302 TIANMSPEYGATCGFFPIDAVTLDYMRLTGRSEEQVALVEAYAKAQGMWRQPGDEPVFTSTLALDMGTVEA 372
                                             *********************************************************************** PP

                               TIGR01341 356 svaGpkrpqdrvalkevkaafkss..lesnagekglalrkeakekklegkeaelkdgavviaaitsctnts 424
                                             s+aGpkrpqdrval +v++af++s  le+n ++k+    k++ +++l+g++++l dgavviaaitsctnts
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 373 SLAGPKRPQDRVALGDVPQAFAASseLEVNHAQKD----KRPIDYTLNGQQYSLPDGAVVIAAITSCTNTS 439
                                             *********************98845777777777....******************************** PP

                               TIGR01341 425 npsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGp 495
                                             npsvl++agllakkave Glk +p+vk+slapGskvv+dyla+++l+p+l+elGfnlvGyGcttciGnsGp
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 440 NPSVLMAAGLLAKKAVERGLKPQPWVKASLAPGSKVVSDYLAHAKLTPWLDELGFNLVGYGCTTCIGNSGP 510
                                             *********************************************************************** PP

                               TIGR01341 496 leeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkk 566
                                             l++ +e aik++dl+v avlsGnrnfegrihplvk+n+laspplvvayalaG++++dl++ep+gt+kdG++
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 511 LPDPIERAIKQGDLTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNLDLTREPLGTGKDGQP 581
                                             *********************************************************************** PP

                               TIGR01341 567 vylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelkl 637
                                             vylkdiwps  e+a++  ++v++e+f+key+ev+eg+++w+ ++v +sd+y+w+++styir++pff+e+ +
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 582 VYLKDIWPSGIEVAQA-VEQVSTEMFRKEYAEVFEGTAEWKAIKVDRSDTYDWQNDSTYIRLSPFFDEMGV 651
                                             **************95.578*************************************************** PP

                               TIGR01341 638 epeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfa 708
                                             ep+ vedi+garil++lGds+ttdhispaGsik dspa++yl+++Gver dfnsyGsrrGnhevm+rGtfa
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 652 EPKPVEDIHGARILAMLGDSVTTDHISPAGSIKADSPAGRYLQNHGVERIDFNSYGSRRGNHEVMMRGTFA 722
                                             *********************************************************************** PP

                               TIGR01341 709 niriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkav 779
                                             niri+n++v+g eGg+t++lpd++ +++ydaam yk+eg+pl+v+aGkeyGsGssrdwaakg++llGv++v
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 723 NIRIRNEMVPGVEGGMTRHLPDTQPIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDWAAKGPRLLGVRVV 793
                                             *********************************************************************** PP

                               TIGR01341 780 iaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveav 850
                                             iaesferihrsnl+gmG+lplef+qg +++tlgl+gee+id+++++ l+p+ +v+v+l+++dg +e+++++
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 794 IAESFERIHRSNLIGMGILPLEFPQGMTRKTLGLNGEERIDISNLQALQPGMTVPVTLTRADGRQEVIDCR 864
                                             *********************************************************************** PP

                               TIGR01341 851 lridtevelayvkkgGilqyvlrkll 876
                                             +ridt++el+y++++Gil+yv+r++l
  lcl|FitnessBrowser__Koxy:BWI76_RS11940 865 CRIDTATELTYYQNDGILHYVIRNML 890
                                             ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (876 nodes)
Target sequences:                          1  (890 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.06
# Mc/sec: 11.16
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory