Alignments for a candidate for cimA in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Desulfacinum hydrothermale DSM 13146

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_084055852.1 B9A12_RS01955 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_900176285.1:WP_084055852.1
          Length = 532

 Score =  665 bits (1716), Expect = 0.0
 Identities = 320/526 (60%), Positives = 414/526 (78%), Gaps = 1/526 (0%)

Query: 1   MSLVKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDI 60
           M  V +YDTTLRDGTQAED +  + DKIR+A KLD++GI YIEGGWPGSNPKD  FF++I
Sbjct: 1   MRRVSIYDTTLRDGTQAEDFNLSLADKIRVALKLDDLGIDYIEGGWPGSNPKDQGFFEEI 60

Query: 61  KKEKLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLE 120
           +  +L  AKI AFG+T      P+KD NL+ L+ A+  V T+FGK+W  HV +AL+ISLE
Sbjct: 61  RNYELKHAKITAFGATHHPGTRPEKDANLRALLDAKTRVITLFGKSWTIHVKDALKISLE 120

Query: 121 ENLELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNG 180
            NLELI DSL YL+ +V  +FYDAEHFFDG++A+PDYA+ TL+ A +  A+C++LCDTNG
Sbjct: 121 RNLELIRDSLAYLRPHVETLFYDAEHFFDGFRADPDYALATLEKAVEGGAECLILCDTNG 180

Query: 181 GTMPFELVEIIREVRKHIT-APLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERC 239
           G +P  + E +R V++     PLGIH HNDS+ AVANSL AV  G VQVQGT NG GERC
Sbjct: 181 GNLPSFIEEAMRAVQQRFPHVPLGIHAHNDSDVAVANSLKAVEMGAVQVQGTFNGVGERC 240

Query: 240 GNANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKG 299
           GNANLCSIIP L LKM   C+  D+++KLR +SRF+ ELAN+ PN++Q YVG SAFAHKG
Sbjct: 241 GNANLCSIIPNLCLKMNVACLEPDRVKKLRSVSRFILELANMPPNRYQPYVGRSAFAHKG 300

Query: 300 GVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEI 359
           GVH++A++R+P TYEH+ PE VGN  R L+S++SG++ +  KA+E+ I + S DPV LE+
Sbjct: 301 GVHIAAVERNPATYEHINPEQVGNRRRFLISEVSGKAAVRYKADEYGIPLSSTDPVALEV 360

Query: 360 LENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLSEATI 419
           L+ IKE+E +GYQFE AEASFELL+ RA+G ++++F +IGFRV+D+K  ED++P+SEATI
Sbjct: 361 LKQIKELEYQGYQFEAAEASFELLLNRAMGRYKRYFELIGFRVVDQKMSEDEEPVSEATI 420

Query: 420 MVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTASSI 479
            V+VGG+ EHTAA G+GPVNALDNALRKALEKFYP LK V+L DYKVRVLP  +GTAS +
Sbjct: 421 RVRVGGQEEHTAALGHGPVNALDNALRKALEKFYPELKGVELSDYKVRVLPGKEGTASKV 480

Query: 480 RVLIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSEEIEG 525
           RVLIES D +  WGTVGVS +I++AS+QAL+DS+ YK++ SE+ +G
Sbjct: 481 RVLIESFDGKEHWGTVGVSHDILEASWQALVDSINYKMYMSEQGKG 526


Lambda     K      H
   0.317    0.135    0.387 

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: 851
Number of extensions: 33
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: 528
Length of database: 532
Length adjustment: 35
Effective length of query: 493
Effective length of database: 497
Effective search space:   245021
Effective search space used:   245021
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: 52 (24.6 bits)

Align candidate WP_084055852.1 B9A12_RS01955 (citramalate synthase)
to HMM TIGR00977 (cimA: citramalate synthase (EC 2.3.1.182))

# 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/TIGR00977.hmm
# target sequence database:        /tmp/gapView.23302.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00977  [M=526]
Accession:   TIGR00977
Description: citramal_synth: citramalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-235  766.5   0.0   6.2e-235  766.3   0.0    1.0  1  lcl|NCBI__GCF_900176285.1:WP_084055852.1  B9A12_RS01955 citramalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176285.1:WP_084055852.1  B9A12_RS01955 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  766.3   0.0  6.2e-235  6.2e-235       2     523 ..       4     524 ..       3     527 .. 0.98

  Alignments for each domain:
  == domain 1  score: 766.3 bits;  conditional E-value: 6.2e-235
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               + +ydttlrdG+qae   lsl dkir+a klddlGi+yieGGwpg+npkd  ffe++++ +lk+ak++a
  lcl|NCBI__GCF_900176285.1:WP_084055852.1   4 VSIYDTTLRDGTQAEDFNLSLADKIRVALKLDDLGIDYIEGGWPGSNPKDQGFFEEIRNYELKHAKITA 72 
                                               78******************************************************************* PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f++t  p  + e+d++l+al++a+t+v+t+fGksw +hv++alk +le nl++i d+++yl+ +++ + 
  lcl|NCBI__GCF_900176285.1:WP_084055852.1  73 FGATHHPGTRPEKDANLRALLDAKTRVITLFGKSWTIHVKDALKISLERNLELIRDSLAYLRPHVETLF 141
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahnd 208
                                               ydaehffdG++a+p+yal+tl+ a ++Ga++l+l+dtnGG lp  iee ++ v++r+ +  lGihahnd
  lcl|NCBI__GCF_900176285.1:WP_084055852.1 142 YDAEHFFDGFRADPDYALATLEKAVEGGAECLILCDTNGGNLPSFIEEAMRAVQQRFPHVPLGIHAHND 210
                                               *********************************************************9999******** PP

                                 TIGR00977 209 setavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvaei 277
                                               s++avansl ave GavqvqGt nG+GercGnanlcs+ipnl lk+++ ++e++++kkl +v+r++ e+
  lcl|NCBI__GCF_900176285.1:WP_084055852.1 211 SDVAVANSLKAVEMGAVQVQGTFNGVGERCGNANLCSIIPNLCLKMNVACLEPDRVKKLRSVSRFILEL 279
                                               ********************************************************************* PP

                                 TIGR00977 278 vnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGi 346
                                                n+++++  pyvG+safahkGGvh++av+rnp tyehi+pe vGn+r+  +se +Gk+ v  k++e+Gi
  lcl|NCBI__GCF_900176285.1:WP_084055852.1 280 ANMPPNRYQPYVGRSAFAHKGGVHIAAVERNPATYEHINPEQVGNRRRFLISEVSGKAAVRYKADEYGI 348
                                               ********************************************************************* PP

                                 TIGR00977 347 eidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdeeslsea 415
                                                +   +p   ++lk+ikele qGy+feaaeas+ell+++a+G+ k+yfe+ gfrv+ +k  ++e  + +
  lcl|NCBI__GCF_900176285.1:WP_084055852.1 349 PLSSTDPVALEVLKQIKELEYQGYQFEAAEASFELLLNRAMGRYKRYFELIGFRVVDQKMSEDE-EPVS 416
                                               *******************************************************999988775.5778 PP

                                 TIGR00977 416 eatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvlie 484
                                               eat+rv v g+ee+taa+G+Gpv+ald+alrkalekfyp+lk ++l dykvr+l ++ Gt +k+rvlie
  lcl|NCBI__GCF_900176285.1:WP_084055852.1 417 EATIRVRVGGQEEHTAALGHGPVNALDNALRKALEKFYPELKGVELSDYKVRVLPGKEGTASKVRVLIE 485
                                               889999999************************************************************ PP

                                 TIGR00977 485 ssdGkrrwgtvGvseniieasytallesieyklrkdeee 523
                                               s dGk +wgtvGvs++i+eas++al++si+yk+   e++
  lcl|NCBI__GCF_900176285.1:WP_084055852.1 486 SFDGKEHWGTVGVSHDILEASWQALVDSINYKMYMSEQG 524
                                               ********************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (532 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.93
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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