Alignments for a candidate for leuC in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfotalea psychrophila LSv54

Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_011189198.1 DP_RS10015 3-isopropylmalate dehydratase large subunit

Query= BRENDA::P81291
         (424 letters)



>NCBI__GCF_000025945.1:WP_011189198.1
          Length = 427

 Score =  323 bits (829), Expect = 5e-93
 Identities = 182/428 (42%), Positives = 254/428 (59%), Gaps = 10/428 (2%)

Query: 1   MGMTIVEKILAKASGKKEVSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPEKI 60
           MG TI EKI   A  + + SP ++V+ N+D  + H+IT P+ +  L E G+++V++  KI
Sbjct: 1   MGKTIAEKIF-DAHLRDKPSPDNMVL-NLDAVLCHEITTPIAIMDLVEKGMDQVFDNTKI 58

Query: 61  VILFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDI-REGVCHQVLPEKGHVAPGEVVV 119
             + DH  PA   K A    +MR + K   IK F+DI   GVCH + PEKG + PG  V+
Sbjct: 59  KAVIDHVTPAKDSKTALQGKIMRDWAKRHAIKDFFDIGANGVCHALFPEKGFIRPGYTVI 118

Query: 120 GADSHTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTSKDVIL 179
             DSHTCTHGAFGAFA G+G+TD+      G   F+ P+++   ++G+LQ  VT+KDVIL
Sbjct: 119 MGDSHTCTHGAFGAFAAGVGTTDLEVGIYKGVCSFRTPKSLKIELSGELQHGVTAKDVIL 178

Query: 180 SIIGEVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVKE 239
           ++I  + V+G T K  +F G  +   ++A RMT+ NMAIE G   GI  PD  T +Y+ E
Sbjct: 179 AVIKRLTVNGGTDKIIEFVGPVIDAFNMAERMTLCNMAIEAGATCGICLPDLVTAEYLWE 238

Query: 240 AMKKHGTE-----RPFEVIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVKQAREVAGK 294
            +K   ++       F     D DA + E  +I+   + P        D VK   ++AG 
Sbjct: 239 FIKDDYSDIAAAVADFSKWHSDSDALYVEEIKIDVSPLTPQVTFDFKPDQVKDITDMAGT 298

Query: 295 PIDQVFIGSCTNGRLEDLRMAIKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFL 354
            +DQ++IGSCTNGR+EDLR A  I+ K   +A  VR +VTPA+ + Y  AL+EGII+ F+
Sbjct: 299 KVDQIYIGSCTNGRIEDLRAAASIL-KGRTLATGVRGIVTPATPKIYSMALEEGIIKIFM 357

Query: 355 KYGCVVTNPSCSACMGSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAV 414
             G  V NP+C AC+G   GVL  GEVC ST+NRNF GR G     ++L SP +A   AV
Sbjct: 358 DAGFCVLNPTCGACLGMSSGVLAEGEVCASTTNRNFNGRMGK-GGMVHLMSPYSATVGAV 416

Query: 415 KGELVDPR 422
            G + DPR
Sbjct: 417 TGTITDPR 424


Lambda     K      H
   0.318    0.136    0.400 

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: 506
Number of extensions: 33
Number of successful extensions: 4
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: 424
Length of database: 427
Length adjustment: 32
Effective length of query: 392
Effective length of database: 395
Effective search space:   154840
Effective search space used:   154840
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: 51 (24.3 bits)

Align candidate WP_011189198.1 DP_RS10015 (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.3165406.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-132  428.2   1.1   1.6e-132  428.0   1.1    1.0  1  NCBI__GCF_000025945.1:WP_011189198.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025945.1:WP_011189198.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.0   1.1  1.6e-132  1.6e-132       1     411 []       3     425 ..       3     425 .. 0.96

  Alignments for each domain:
  == domain 1  score: 428.0 bits;  conditional E-value: 1.6e-132
                             TIGR02086   1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPaptveaa 72 
                                           kt+aeki+ ++   + ++ ++ + + D v+ h+ t+p +i  l e g ++v++++ki  v+Dhv+Pa++ ++a
  NCBI__GCF_000025945.1:WP_011189198.1   3 KTIAEKIFDAHLRDKPSPDNM-VLNLDAVLCHEITTPIAIMDLVEKGmDQVFDNTKIKAVIDHVTPAKDSKTA 74 
                                           599********8777776555.5689***************999988899*********************** PP

                             TIGR02086  73 elqkeirefakelgikv.fdvg.eGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatDvalala 143
                                              k +r++ak++ ik  fd+g +G+ch ++ ekg+++pg+ v+ +Dsht+t+Ga+gafa G+G+tD+ + + 
  NCBI__GCF_000025945.1:WP_011189198.1  75 LQGKIMRDWAKRHAIKDfFDIGaNGVCHALFPEKGFIRPGYTVIMGDSHTCTHGAFGAFAAGVGTTDLEVGIY 147
                                           *****************9998637************************************************* PP

                             TIGR02086 144 tGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRltlsnlaveag 216
                                            G   ++ P+s+k+el+G+l++ vtakDvil ++k+l+ +g t k ief g +i+a+++ eR+tl+n+a+eag
  NCBI__GCF_000025945.1:WP_011189198.1 148 KGVCSFRTPKSLKIELSGELQHGVTAKDVILAVIKRLTVNGGTDKIIEFVGPVIDAFNMAERMTLCNMAIEAG 220
                                           ************************************************************************* PP

                             TIGR02086 217 akaglvepdeetleylkkrrge...........frilkadedakyeeeieidlseleplvavPhsvdnvkeve 278
                                           a  g+  pd  t eyl +  ++           f   ++d da y+eei+id+s l+p+v+  +++d+vk+++
  NCBI__GCF_000025945.1:WP_011189198.1 221 ATCGICLPDLVTAEYLWEFIKDdysdiaaavadFSKWHSDSDALYVEEIKIDVSPLTPQVTFDFKPDQVKDIT 293
                                           *********99999987766655677999999889999*********************************** PP

                             TIGR02086 279 evegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlveaGaiiltp 351
                                           ++ gt++dq++iGsCtnGR+edl++aa il+gr+ ++ vr iv+Pa  k+y  aleeG+i+++++aG  +l+p
  NCBI__GCF_000025945.1:WP_011189198.1 294 DMAGTKVDQIYIGSCTNGRIEDLRAAASILKGRTLATGVRGIVTPATPKIYSMALEEGIIKIFMDAGFCVLNP 366
                                           ************************************************************************* PP

                             TIGR02086 352 gCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpee 411
                                           +CG ClG   Gvla+gev+ sttnRnf+GRmG+    ++L sP  a v av+G+itdp++
  NCBI__GCF_000025945.1:WP_011189198.1 367 TCGACLGMSSGVLAEGEVCASTTNRNFNGRMGKG-GMVHLMSPYSATVGAVTGTITDPRQ 425
                                           ********************************75.78*********************86 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 19.00
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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