Alignments for a candidate for leuC in Geobacter metallireducens GS-15

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Geobacter metallireducens GS-15

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_004512099.1 GMET_RS06385 3-isopropylmalate dehydratase large subunit

Query= reanno::DvH:208495
         (419 letters)



>NCBI__GCF_000012925.1:WP_004512099.1
          Length = 427

 Score =  357 bits (915), Expect = e-103
 Identities = 192/426 (45%), Positives = 264/426 (61%), Gaps = 13/426 (3%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           M  T A+KI   H  +      +++R  + +V+ ++IT P+AI    A G  RVFD  ++
Sbjct: 1   MGKTTAEKIFASHLVDEPFSGTKVLR--LDVVMCHEITTPIAIADLMARGKDRVFDPTKI 58

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
             V+DH TP KD + A Q K+ R++AR   +  +++ G  GV HAL PE G + PG  V+
Sbjct: 59  KAVIDHVTPSKDSKTATQAKMLRDWARRHAIKDFFDVGHNGVCHALFPEKGYIRPGYTVI 118

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
             DSHTCT+G  GAFA G+G+TD+   +  G   F+ P +IR    GTLP  V AKD+IL
Sbjct: 119 MGDSHTCTHGAFGAFAAGVGTTDLEVGILKGVCAFREPKSIRINLNGTLPKGVYAKDVIL 178

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTY--- 237
            +IG +GV+GA  R +EF G  ++A+ +E RMT+ NMAIEAGG +G+   D  T+ Y   
Sbjct: 179 YVIGQLGVNGATDRVMEFRGPVVDAMTMESRMTLCNMAIEAGGTSGICMPDMVTVEYLWP 238

Query: 238 -------CTTAGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDV 290
                     A     + + +D  AVYER L FDV+ + P+V   + PD VKP+SE+   
Sbjct: 239 FIENEYPSKEAALAEFSTWRSDDDAVYERVLDFDVSVLEPIVTFGYKPDQVKPISEIAGS 298

Query: 291 TVQQVVIGSCTNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFME 350
            V QV +GSCTNGR+ DLR AA +L+G+K++  VR I+ PATP I++ A+ EGLI+ FME
Sbjct: 299 PVDQVYLGSCTNGRLEDLRIAARILKGKKIAPSVRGILSPATPKIYKDAMAEGLIDIFME 358

Query: 351 AGCIVGPATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVT 410
           AG  V   TCG CLG   G+LA+GE   +TTNRNF GRMG     V+L  PAT+AA+A+ 
Sbjct: 359 AGFCVTNPTCGACLGMSNGVLAEGEVCASTTNRNFMGRMGK-GGMVHLMSPATSAATAIE 417

Query: 411 GVITDP 416
           GVI DP
Sbjct: 418 GVIADP 423


Lambda     K      H
   0.320    0.136    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: 460
Number of extensions: 15
Number of successful extensions: 3
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: 419
Length of database: 427
Length adjustment: 32
Effective length of query: 387
Effective length of database: 395
Effective search space:   152865
Effective search space used:   152865
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_004512099.1 GMET_RS06385 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02086 (3-isopropylmalate dehydratase, large subunit)

# 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.aa/TIGR02086.hmm
# target sequence database:        /tmp/gapView.16938.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02086  [M=411]
Accession:   TIGR02086
Description: IPMI_arch: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-135  437.0   0.2   3.5e-135  436.8   0.2    1.0  1  lcl|NCBI__GCF_000012925.1:WP_004512099.1  GMET_RS06385 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012925.1:WP_004512099.1  GMET_RS06385 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.8   0.2  3.5e-135  3.5e-135       2     410 ..       4     424 ..       3     425 .. 0.96

  Alignments for each domain:
  == domain 1  score: 436.8 bits;  conditional E-value: 3.5e-135
                                 TIGR02086   2 tlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPaptv 69 
                                               t aeki++++   e  +G  v+ + D+vm h+ t+p +i  l   g ++v++++ki  v+Dhv+P+++ 
  lcl|NCBI__GCF_000012925.1:WP_004512099.1   4 TTAEKIFASHLVDEPFSGTKVL-RLDVVMCHEITTPIAIADLMARGkDRVFDPTKIKAVIDHVTPSKDS 71 
                                               789******9999999999986.89***************99998889********************* PP

                                 TIGR02086  70 eaaelqkeirefakelgikv.fdvg.eGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGat 136
                                               ++a   k++r++a+++ ik  fdvg +G+ch ++ ekgy++pg+ v+ +Dsht+t+Ga+gafa G+G+t
  lcl|NCBI__GCF_000012925.1:WP_004512099.1  72 KTATQAKMLRDWARRHAIKDfFDVGhNGVCHALFPEKGYIRPGYTVIMGDSHTCTHGAFGAFAAGVGTT 140
                                               ********************9998747****************************************** PP

                                 TIGR02086 137 DvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeR 205
                                               D+ + ++ G   ++ P+si+++l+G l + v+akDvil ++++lg +gat +++ef g +++a+++++R
  lcl|NCBI__GCF_000012925.1:WP_004512099.1 141 DLEVGILKGVCAFREPKSIRINLNGTLPKGVYAKDVILYVIGQLGVNGATDRVMEFRGPVVDAMTMESR 209
                                               ********************************************************************* PP

                                 TIGR02086 206 ltlsnlaveagakaglvepdeetleylkkrrge...........frilkadedakyeeeieidlselep 263
                                               +tl+n+a+eag+ +g+  pd  t+eyl    ++           f   ++d+da ye  +++d+s lep
  lcl|NCBI__GCF_000012925.1:WP_004512099.1 210 MTLCNMAIEAGGTSGICMPDMVTVEYLWPFIENeypskeaalaeFSTWRSDDDAVYERVLDFDVSVLEP 278
                                               *************************99654444456688899999999********************* PP

                                 TIGR02086 264 lvavPhsvdnvkeveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyeka 332
                                                v+  +++d+vk+++e+ g  +dqv++GsCtnGRledl+iaa+il+g++ +++vr i +Pa  k+y++a
  lcl|NCBI__GCF_000012925.1:WP_004512099.1 279 IVTFGYKPDQVKPISEIAGSPVDQVYLGSCTNGRLEDLRIAARILKGKKIAPSVRGILSPATPKIYKDA 347
                                               ********************************************************************* PP

                                 TIGR02086 333 leeGlietlveaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsa 401
                                               + eGli++++eaG  +++p+CG ClG   Gvla+gev+ sttnRnf GRmG+    ++L sPa++a++a
  lcl|NCBI__GCF_000012925.1:WP_004512099.1 348 MAEGLIDIFMEAGFCVTNPTCGACLGMSNGVLAEGEVCASTTNRNFMGRMGKG-GMVHLMSPATSAATA 415
                                               ***************************************************75.78************* PP

                                 TIGR02086 402 veGeitdpe 410
                                               +eG+i+dp+
  lcl|NCBI__GCF_000012925.1:WP_004512099.1 416 IEGVIADPR 424
                                               *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (427 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.88
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis