Alignments for a candidate for glcB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Burkholderia phytofirmans PsJN

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate BPHYT_RS09815 BPHYT_RS09815 malate synthase

Query= reanno::psRCH2:GFF353
         (726 letters)



>FitnessBrowser__BFirm:BPHYT_RS09815
          Length = 724

 Score =  979 bits (2530), Expect = 0.0
 Identities = 476/726 (65%), Positives = 590/726 (81%), Gaps = 10/726 (1%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT+    GGLQVA  L  FV  EA+PGTG+D+AAFW+G D+++H+LAPKNRALLA+RD L
Sbjct: 1   MTQMNTRGGLQVAANLDQFVETEALPGTGIDSAAFWSGFDALVHELAPKNRALLAERDRL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q ++D WH+A  G   D  AY++FL+ IGY++P     +ATT+NVD EIA  AGPQLVVP
Sbjct: 61  QTELDNWHRANPGPVRDLRAYRAFLEGIGYIVPAPASVKATTDNVDTEIAEQAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           + N R+ALNAANARWGSLYDALYGTDAI E  GA K   +N +RG  VIAYAR FL++AA
Sbjct: 121 LSNQRYALNAANARWGSLYDALYGTDAIPETGGAEKQKAFNPVRGAAVIAYARKFLDQAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GSH D+T Y ++GGKLVV+LK+G T+ LK PAQ  G+QGE SAP AVLLK+NG+HF
Sbjct: 181 PLANGSHADATRYSVDGGKLVVTLKNG-TSELKTPAQFIGYQGEESAPSAVLLKHNGLHF 239

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQID +  IG+TDAA VKD+++E+A++TI+DCEDS+AAVDADDK ++YRNWLGLM GDL
Sbjct: 240 EIQIDASDSIGRTDAAHVKDVVVEAAVSTIIDCEDSVAAVDADDKVLLYRNWLGLMTGDL 299

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            EE+ K GK  TR +N DRVYT A+G   + LHGRSLLFIRNVGHLMTN A+L K+G+E+
Sbjct: 300 TEEVTKNGKTFTRRLNADRVYTAANGTAPVVLHGRSLLFIRNVGHLMTNPAVLTKDGHEI 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+D + T+L A+H+      + N+RTGS+YIVKPKMHGP EVAFA+ELF RVED+L 
Sbjct: 360 PEGILDAVITTLCALHD---RKHQLNSRTGSIYIVKPKMHGPAEVAFASELFSRVEDLLK 416

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           LPRNT+K+GIMDEERRT++NL ACI EA ERV FINTGFLDRTGDE+H++MEAGPM+RK 
Sbjct: 417 LPRNTIKMGIMDEERRTSVNLLACIAEASERVAFINTGFLDRTGDEMHSAMEAGPMMRKG 476

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MK+  WI+AYE +NV VGL+ GL+G++QIGKGMWAMPDLM AMLEQK+ HP AGANTAW
Sbjct: 477 DMKSSAWIAAYERSNVLVGLSAGLRGRSQIGKGMWAMPDLMHAMLEQKIAHPKAGANTAW 536

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASI-----DDILTIPLAQDTNWSEEEKRN 595
           VPSPTAATLHA+HYH++DVQA Q EL + + A++     D +LTIP+  +  WS++E R+
Sbjct: 537 VPSPTAATLHALHYHQVDVQAVQRELERTDYATVRDELLDGLLTIPVVAEAKWSDDEIRS 596

Query: 596 ELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKD 655
           E+DNN+QGILGY+VRW++QGVGCSKVPDI+D+ LMEDRATLRISSQH+ANW+ HGVV ++
Sbjct: 597 EIDNNAQGILGYVVRWIDQGVGCSKVPDIHDVGLMEDRATLRISSQHIANWLYHGVVKRE 656

Query: 656 QVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHR 715
            V E+ KRMA VVD QN GDPLY+PMAP FD ++AF+AA  LV EG +QP+GYTEP+LH+
Sbjct: 657 LVEETFKRMAKVVDEQNAGDPLYKPMAPGFD-TIAFKAAQALVFEGRQQPSGYTEPLLHK 715

Query: 716 RRREFK 721
            R E K
Sbjct: 716 FRLEVK 721


Lambda     K      H
   0.316    0.133    0.386 

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: 1463
Number of extensions: 67
Number of successful extensions: 5
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: 726
Length of database: 724
Length adjustment: 40
Effective length of query: 686
Effective length of database: 684
Effective search space:   469224
Effective search space used:   469224
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: 55 (25.8 bits)

Align candidate BPHYT_RS09815 BPHYT_RS09815 (malate synthase)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

# 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/TIGR01345.hmm
# target sequence database:        /tmp/gapView.12245.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01345  [M=721]
Accession:   TIGR01345
Description: malate_syn_G: malate synthase G
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 1202.1   0.0          0 1201.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS09815  BPHYT_RS09815 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS09815  BPHYT_RS09815 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1201.9   0.0         0         0       3     719 ..       5     722 ..       3     724 .] 0.98

  Alignments for each domain:
  == domain 1  score: 1201.9 bits;  conditional E-value: 0
                                TIGR01345   3 vdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.g 71 
                                               + g+lqva++l +fve e+lpgtg+d+++fwsgfd++v++lap+nr lla+rd++q+ +d++hr n+ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815   5 NTRGGLQVAANLDQFVETEALPGTGIDSAAFWSGFDALVHELAPKNRALLAERDRLQTELDNWHRANPgP 74 
                                              6789****************************************************************77 PP

                                TIGR01345  72 vidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalyg 141
                                              v d  ay+ fl+ igy+v+ p  v+ +t+nvd+eia qagpqlvvp+ n ryalnaanarwgslydalyg
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815  75 VRDLRAYRAFLEGIGYIVPAPASVKATTDNVDTEIAEQAGPQLVVPLSNQRYALNAANARWGSLYDALYG 144
                                              89******************************************************************** PP

                                TIGR01345 142 snvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkd 211
                                              +++ipe++gaek k +np+rg  vi++ar+fld++ pl +gs+ad+ +y++  +kl+v+l++g +  lk+
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 145 TDAIPETGGAEKQKAFNPVRGAAVIAYARKFLDQAAPLANGSHADATRYSVDGGKLVVTLKNG-TSELKT 213
                                              *************************************************************76.578*** PP

                                TIGR01345 212 eeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaed 281
                                              ++qf+gy+g+ ++p+++llk+nglh e+qida + ig++d a+vkd+v+e+a++ti+dcedsvaavda+d
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 214 PAQFIGYQGEESAPSAVLLKHNGLHFEIQIDASDSIGRTDAAHVKDVVVEAAVSTIIDCEDSVAAVDADD 283
                                              ********************************************************************** PP

                                TIGR01345 282 kvlvyrnllglmkgtlkeklekngriikrklnedrsytaangee.lslhgrsllfvrnvghlmtipvilt 350
                                              kvl+yrn+lglm+g+l e+++kng++++r+ln dr+ytaang+  ++lhgrsllf+rnvghlmt+p++lt
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 284 KVLLYRNWLGLMTGDLTEEVTKNGKTFTRRLNADRVYTAANGTApVVLHGRSLLFIRNVGHLMTNPAVLT 353
                                              ******************************************96599*********************** PP

                                TIGR01345 351 degeeipegildgvltsvialydlkvqnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerh 420
                                              ++g+eipegild+v+t+++al+d k+q    nsr+gs+yivkpkmhgp evafa +lf+r+edll l+r+
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 354 KDGHEIPEGILDAVITTLCALHDRKHQL---NSRTGSIYIVKPKMHGPAEVAFASELFSRVEDLLKLPRN 420
                                              ***********************99965...*************************************** PP

                                TIGR01345 421 tlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayern 490
                                              t+k+g+mdeerrts+nl acia++ ervafintgfldrtgde+h++meag+m+rk+dmks++w+ ayer+
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 421 TIKMGIMDEERRTSVNLLACIAEASERVAFINTGFLDRTGDEMHSAMEAGPMMRKGDMKSSAWIAAYERS 490
                                              ********************************************************************** PP

                                TIGR01345 491 nvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqk 560
                                              nv+ gl +glrg++qigkgmwampdlm  mle+k+  ++agantawvpsptaatlhalhyh+vdvq+vq 
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 491 NVLVGLSAGLRGRSQIGKGMWAMPDLMHAMLEQKIAHPKAGANTAWVPSPTAATLHALHYHQVDVQAVQR 560
                                              ********************************************************************** PP

                                TIGR01345 561 eladaerrae....lkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnval 626
                                              el  ++  +     l+ +ltipv  +++ws++ei+ e+dnn+qgilgyvvrw++qg+gcskvpdih+v l
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 561 ELERTDYATVrdelLDGLLTIPVVAEAKWSDDEIRSEIDNNAQGILGYVVRWIDQGVGCSKVPDIHDVGL 630
                                              **99987766344567789*************************************************** PP

                                TIGR01345 627 medratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlil 696
                                              medratlrissqh+anwl hg+v +e v e+++rmakvvd+qnagd+ y+pma+ ++ ++afkaa+ l++
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 631 MEDRATLRISSQHIANWLYHGVVKRELVEETFKRMAKVVDEQNAGDPLYKPMAPGFD-TIAFKAAQALVF 699
                                              ********************************************************8.69********** PP

                                TIGR01345 697 kgtkqpsgytepilharrlefke 719
                                              +g +qpsgytep+lh+ rle k+
  lcl|FitnessBrowser__BFirm:BPHYT_RS09815 700 EGRQQPSGYTEPLLHKFRLEVKK 722
                                              ********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (724 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 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 7.14
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources