GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Pedobacter sp. GW460-11-11-14-LB5

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate CA265_RS16405 CA265_RS16405 aconitate hydratase

Query= BRENDA::Q8RP87
         (747 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS16405 CA265_RS16405 aconitate
           hydratase
          Length = 759

 Score =  985 bits (2547), Expect = 0.0
 Identities = 485/747 (64%), Positives = 574/747 (76%), Gaps = 2/747 (0%)

Query: 1   MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60
           M +D++M+K  YA++  ++E  R  + RPLTL+EKILY HL++      ++RG DYV+F 
Sbjct: 1   MAFDIDMIKKVYANFGSRVEAARKVVGRPLTLSEKILYAHLWDGDPKTAFKRGSDYVDFA 60

Query: 61  PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120
           PDRVAMQDATAQMALLQFM AG+  VAVPSTVHCDHLI A  GA  D+  A   + EV+D
Sbjct: 61  PDRVAMQDATAQMALLQFMQAGRPQVAVPSTVHCDHLITAKEGAAIDLPHAKTESAEVFD 120

Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
           FL  VS++YGIGFWKPGAGIIHQVVLENYAFPGGMM+GTDSHT NAGGLGMVAIGVGGAD
Sbjct: 121 FLSSVSNKYGIGFWKPGAGIIHQVVLENYAFPGGMMIGTDSHTVNAGGLGMVAIGVGGAD 180

Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
           A DVM G+ WELK PKLIGV+LTG+LNGWTA KDVILK+AGILTVKGGT AI+EYFG G 
Sbjct: 181 ACDVMAGLPWELKFPKLIGVKLTGKLNGWTAAKDVILKVAGILTVKGGTGAIVEYFGDGA 240

Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300
            S+S TGK TICNMGAE+GATTS F YDE M  YL+ATGR EVA  A+ +AA L  D EV
Sbjct: 241 TSMSCTGKGTICNMGAEIGATTSTFGYDESMERYLRATGRNEVADEANKIAAYLTGDAEV 300

Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPISEFAEKVVTNGYPRKMEVGLIGSCT 360
            A P++++D+VIEI+L  LEPY+NGPFTPD ATP+S+   +   NG+P K+E GLIGSCT
Sbjct: 301 YADPENYFDQVIEIDLDTLEPYLNGPFTPDLATPVSQMKVEAEKNGWPLKVEWGLIGSCT 360

Query: 361 NSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMAN 420
           NSSY+D+SRA S+A Q   K L   A   +NPGSEQ+R TA+RDG +  FE + ATI  N
Sbjct: 361 NSSYEDLSRAASIANQAIAKGLVTKADFGINPGSEQVRYTADRDGFLKTFEDLNATIFTN 420

Query: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGDLC 480
           ACGPCIG W R   +   KN+IV SFNRNFAKRADGNPNTFAFVASPE+V A+ I+G+L 
Sbjct: 421 ACGPCIGMWDRTGAEKAEKNTIVHSFNRNFAKRADGNPNTFAFVASPEMVAAIAISGNLG 480

Query: 481 FNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAPG--GEKNEIRVAPDSQRLQ 538
           FNPL D L N  GE+VKL  P G ELP+ GF   + GYQAP   G   ++ V+P S RLQ
Sbjct: 481 FNPLTDTLTNDKGEQVKLDPPTGFELPTKGFAVEDAGYQAPAADGSSVQVLVSPTSHRLQ 540

Query: 539 LLTPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFN 598
           LL PF  W+G D   + LLIKA+GKCTTDHISMAGPWL+FRGHL+NIS+NML+GAVN FN
Sbjct: 541 LLDPFTPWEGTDLQGLKLLIKAKGKCTTDHISMAGPWLKFRGHLDNISNNMLIGAVNYFN 600

Query: 599 GETNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVKVI 658
            +T+ V N LT  Y  V  T + YKA G+ SIVV +ENYGEGSSREHAAMEPR L V+ +
Sbjct: 601 DKTDNVKNELTGEYGPVPATQRDYKAAGLGSIVVGDENYGEGSSREHAAMEPRHLGVRAV 660

Query: 659 LAKSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHHED 718
           L KSFARIHETNLKKQGML +TFADK DYD+I E D I ++GL EF+P + L ++LHH D
Sbjct: 661 LVKSFARIHETNLKKQGMLGLTFADKDDYDKILEDDTIDILGLTEFTPDQPLTLVLHHAD 720

Query: 719 GTEERFAVQHTYNEQQIGWFRAGSALN 745
           GT+E F V H+YN QQI WF+AG ALN
Sbjct: 721 GTQESFPVNHSYNAQQIDWFKAGGALN 747


Lambda     K      H
   0.317    0.134    0.395 

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: 1540
Number of extensions: 53
Number of successful extensions: 2
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: 747
Length of database: 759
Length adjustment: 40
Effective length of query: 707
Effective length of database: 719
Effective search space:   508333
Effective search space used:   508333
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 (21.7 bits)
S2: 55 (25.8 bits)

Align candidate CA265_RS16405 CA265_RS16405 (aconitate hydratase)
to HMM TIGR01340 (aconitate hydratase, mitochondrial (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/TIGR01340.hmm
# target sequence database:        /tmp/gapView.10576.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01340  [M=745]
Accession:   TIGR01340
Description: aconitase_mito: aconitate hydratase, mitochondrial
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 1106.2   0.0          0 1106.0   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS16405  CA265_RS16405 aconitate hydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS16405  CA265_RS16405 aconitate hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1106.0   0.0         0         0       1     745 []      12     749 ..      12     749 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1106.0 bits;  conditional E-value: 0
                                  TIGR01340   1 yekllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqm 68 
                                                y+++ ++++  r+v++ rpltl+ek+ly+hl d +           rG+ y+ + pdrvamqda+aqm
  lcl|FitnessBrowser__Pedo557:CA265_RS16405  12 YANFGSRVEAARKVVG-RPLTLSEKILYAHLWDGDP---KTAF--KRGSDYVDFAPDRVAMQDATAQM 73 
                                                667778999999*999.****************998...3444..5********************** PP

                                  TIGR01340  69 allqflsaglkkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGii 136
                                                allqf+ ag ++vavp++vhcdhli ak+G+  dl++ak    evfdfl s+++kygi+fwkpG+Gii
  lcl|FitnessBrowser__Pedo557:CA265_RS16405  74 ALLQFMQAGRPQVAVPSTVHCDHLITAKEGAAIDLPHAKTESAEVFDFLSSVSNKYGIGFWKPGAGII 141
                                                ******************************************************************** PP

                                  TIGR01340 137 hqivlenyavpGllmlGtdshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgw 204
                                                hq+vlenya+pG++m+Gtdsht naGGl+++aiGvGGada dv+ag+pwelk pk++GvkltGkl+gw
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 142 HQVVLENYAFPGGMMIGTDSHTVNAGGLGMVAIGVGGADACDVMAGLPWELKFPKLIGVKLTGKLNGW 209
                                                ******************************************************************** PP

                                  TIGR01340 205 tspkdvilklaglltvkGGtGaiveyfGeGveslsctGmaticnmGaeiGattslfpfneaskdylka 272
                                                t++kdvilk+ag+ltvkGGtGaiveyfG+G  s+sctG +ticnmGaeiGatts+f ++e++++yl+a
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 210 TAAKDVILKVAGILTVKGGTGAIVEYFGDGATSMSCTGKGTICNMGAEIGATTSTFGYDESMERYLRA 277
                                                ******************************************************************** PP

                                  TIGR01340 273 tnraeiaeeak.vakd..kaellkadkdaeydelieidlsklephvnGpftpdlstpiskfkekvkke 337
                                                t+r+e+a+ea+ +a +      + ad +  +d++ieidl++lep++nGpftpdl+tp+s++k +++k+
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 278 TGRNEVADEANkIAAYltGDAEVYADPENYFDQVIEIDLDTLEPYLNGPFTPDLATPVSQMKVEAEKN 345
                                                *******999854444112344569******************************************* PP

                                  TIGR01340 338 kwpeklkvGliGsctnssyedmsrvasivkdaekaGlkskidftvtpGseqiratlerdgilevfeka 405
                                                +wp k++ GliGsctnssyed+sr+asi+++a  +Gl +k+df + pGseq+r t +rdg l++fe+ 
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 346 GWPLKVEWGLIGSCTNSSYEDLSRAASIANQAIAKGLVTKADFGINPGSEQVRYTADRDGFLKTFEDL 413
                                                ******************************************************************** PP

                                  TIGR01340 406 GgvvlanacGpciGqwdrkdvvkkgekntiltsynrnfrgrndanratmaflaspelvtalsvaGslk 473
                                                 +++++nacGpciG wdr    +k eknti+ s+nrnf  r d+n++t af+aspe+v+a++++G+l 
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 414 NATIFTNACGPCIGMWDRTG-AEKAEKNTIVHSFNRNFAKRADGNPNTFAFVASPEMVAAIAISGNLG 480
                                                *******************9.99********************************************* PP

                                  TIGR01340 474 fnpltdslktkdGkefklkapkGdelpekgfeaGrdtfqaesdspdenvevavdpksdrlqllepfek 541
                                                fnpltd+l++ +G + kl++p+G elp+kgf      +qa++ +  ++v+v v+p+s+rlqll+pf +
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 481 FNPLTDTLTNDKGEQVKLDPPTGFELPTKGFAVEDAGYQAPAAD-GSSVQVLVSPTSHRLQLLDPFTP 547
                                                ******************************************99.9********************** PP

                                  TIGR01340 542 wngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldnisentligavnaetgevnkvkdk.dGskg 608
                                                w+g dl+gl++lik kGkcttdhis+aGpwlk++Ghldnis+n+ligavn+ +++ ++vk++ +G++g
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 548 WEGTDLQGLKLLIKAKGKCTTDHISMAGPWLKFRGHLDNISNNMLIGAVNYFNDKTDNVKNElTGEYG 615
                                                ************************************************************999***** PP

                                  TIGR01340 609 avpelakdykargvkwvvvaeenyGeGsarehaaleprylGgriiivksfarihetnlkkqGvlpltf 676
                                                 vp++ +dyka g   +vv++enyGeGs+rehaa+epr+lG r+++vksfarihetnlkkqG+l ltf
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 616 PVPATQRDYKAAGLGSIVVGDENYGEGSSREHAAMEPRHLGVRAVLVKSFARIHETNLKKQGMLGLTF 683
                                                ******************************************************************** PP

                                  TIGR01340 677 aneadydkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklkhtlskdqieffkaGsalnl 744
                                                a++ dydki  +d++++l+l+e+++   +++++l +++ +g  ++  ++h+ + +qi++fkaG aln 
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 684 ADKDDYDKILEDDTIDILGLTEFTP---DQPLTLVLHHADGTQESFPVNHSYNAQQIDWFKAGGALNI 748
                                                ************************9...99*************************************7 PP

                                  TIGR01340 745 l 745
                                                +
  lcl|FitnessBrowser__Pedo557:CA265_RS16405 749 I 749
                                                5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (745 nodes)
Target sequences:                          1  (759 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 12.87
//
[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