Alignments for a candidate for cimA in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Desulfotomaculum ruminis DSM 2154

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_013840437.1 DESRU_RS01900 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000215085.1:WP_013840437.1
          Length = 530

 Score =  577 bits (1486), Expect = e-169
 Identities = 289/520 (55%), Positives = 374/520 (71%), Gaps = 4/520 (0%)

Query: 3   LVKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKK 62
           L+K+YDT+LRDGTQ E +S   EDK++IA +LDE+G HYIEGGWPGSNPKD+ FF  +++
Sbjct: 10  LIKIYDTSLRDGTQGEGVSLSAEDKMKIARRLDEMGFHYIEGGWPGSNPKDMEFFARLRQ 69

Query: 63  EKLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEEN 122
             L  A + AFGST R  V   +D NL  L+++      IFGKTWDFHV +AL  SLEEN
Sbjct: 70  TPLKNALVTAFGSTCRPGVEAARDENLNRLLESGVRAAAIFGKTWDFHVTKALNTSLEEN 129

Query: 123 LELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGT 182
           L ++ DS+ YLK     VF+D EHFFDG+KANPDYA+  L+AA +  AD +VLCDTNGGT
Sbjct: 130 LRMVRDSVAYLKQQGLTVFFDGEHFFDGFKANPDYALSVLRAAVEGGADAVVLCDTNGGT 189

Query: 183 MPFELVEIIREVRKHIT-APLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGN 241
           +P EL  ++  V++ +    LGIH HND E AVAN++ AV  G+ QVQGT+NG GERCGN
Sbjct: 190 LPHELQSVVARVKQELPGVELGIHAHNDGEMAVANTIVAVQAGVTQVQGTVNGLGERCGN 249

Query: 242 ANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGGV 301
           ANLCSI+P L LK+  E I  +    L +LSRFVYE+ANL+P  +Q +VG SAFAHKGG+
Sbjct: 250 ANLCSILPNLTLKLGYETIPRENFAFLTELSRFVYEVANLNPVNNQPFVGESAFAHKGGI 309

Query: 302 HVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEILE 361
           HVSA+ + P TYEH+ PE VGN  RVL+S+LSG SN+L K +E  + +D   P    +LE
Sbjct: 310 HVSALLKEPGTYEHMPPEWVGNTRRVLMSELSGLSNLLYKYKE--LHLDKSSPEGRRVLE 367

Query: 362 NIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLSEATIMV 421
            +K ME+RGYQFE AE S E+++++A+  +R+ F +   R+I E R ED+   SEA I +
Sbjct: 368 QLKNMEHRGYQFEAAEGSLEIMLRKAVNGYREPFQLESMRLILEMR-EDRPIQSEAVIKL 426

Query: 422 KVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTASSIRV 481
           +VG ++ HTAAEGNGPVNALDNALRKALE  YP +  ++LLDYKVRVL    GT + +RV
Sbjct: 427 RVGEEVVHTAAEGNGPVNALDNALRKALETVYPEVPGLRLLDYKVRVLEEKAGTEAQVRV 486

Query: 482 LIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSE 521
           LIE+G+ +  WGTVGVS NI++AS+QAL D + Y L K E
Sbjct: 487 LIETGNGKKTWGTVGVSTNIIEASWQALADGMAYGLLKDE 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: 776
Number of extensions: 31
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: 528
Length of database: 530
Length adjustment: 35
Effective length of query: 493
Effective length of database: 495
Effective search space:   244035
Effective search space used:   244035
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_013840437.1 DESRU_RS01900 (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.3575.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-230  749.2   0.0   1.1e-229  749.0   0.0    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013840437.1  DESRU_RS01900 citramalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013840437.1  DESRU_RS01900 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  749.0   0.0  1.1e-229  1.1e-229       2     523 ..      11     528 ..      10     530 .] 0.99

  Alignments for each domain:
  == domain 1  score: 749.0 bits;  conditional E-value: 1.1e-229
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               +k+ydt+lrdG+q eGvsls edk++ia++ld++G hyieGGwpg+npkd++ff ++++ +lkna v+a
  lcl|NCBI__GCF_000215085.1:WP_013840437.1  11 IKIYDTSLRDGTQGEGVSLSAEDKMKIARRLDEMGFHYIEGGWPGSNPKDMEFFARLRQTPLKNALVTA 79 
                                               79******************************************************************* PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f+st rp ++   d++l+ l++++ +  +ifGk+wd+hv++al+t+leenl+m+ d+v+ylk+++  v 
  lcl|NCBI__GCF_000215085.1:WP_013840437.1  80 FGSTCRPGVEAARDENLNRLLESGVRAAAIFGKTWDFHVTKALNTSLEENLRMVRDSVAYLKQQGLTVF 148
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahnd 208
                                               +d ehffdG+kanp+yal +l++a ++Gad +vl+dtnGGtlphe++ ++ +vk++l   +lGihahnd
  lcl|NCBI__GCF_000215085.1:WP_013840437.1 149 FDGEHFFDGFKANPDYALSVLRAAVEGGADAVVLCDTNGGTLPHELQSVVARVKQELPGVELGIHAHND 217
                                               ********************************************************************* PP

                                 TIGR00977 209 setavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvaei 277
                                                e+avan+++av+aG +qvqGt+nGlGercGnanlcs++pnl lklg++ i++en++ lte++r+v e+
  lcl|NCBI__GCF_000215085.1:WP_013840437.1 218 GEMAVANTIVAVQAGVTQVQGTVNGLGERCGNANLCSILPNLTLKLGYETIPRENFAFLTELSRFVYEV 286
                                               ********************************************************************* PP

                                 TIGR00977 278 vnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGi 346
                                                nl + +n p+vGesafahkGG+hvsa+ ++p tyeh+ pe vGn r++ +sel+G+sn+l k kel  
  lcl|NCBI__GCF_000215085.1:WP_013840437.1 287 ANLNPVNNQPFVGESAFAHKGGIHVSALLKEPGTYEHMPPEWVGNTRRVLMSELSGLSNLLYKYKEL-- 353
                                               *****************************************************************96.. PP

                                 TIGR00977 347 eidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdeeslsea 415
                                               ++d++sp+ r++l+++k++e++Gy+feaae sle+++r+a+   ++ f+++++r++++ r d    sea
  lcl|NCBI__GCF_000215085.1:WP_013840437.1 354 HLDKSSPEGRRVLEQLKNMEHRGYQFEAAEGSLEIMLRKAVNGYREPFQLESMRLILEMREDRPIQSEA 422
                                               79*******************************************************999999888888 PP

                                 TIGR00977 416 eatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvlie 484
                                                +++rv +e+  ++taaeGnGpv+ald+alrkale  yp++  l+l+dykvr+l+e+aGt+a++rvlie
  lcl|NCBI__GCF_000215085.1:WP_013840437.1 423 VIKLRVGEEV--VHTAAEGNGPVNALDNALRKALETVYPEVPGLRLLDYKVRVLEEKAGTEAQVRVLIE 489
                                               8888888887..59******************************************************* PP

                                 TIGR00977 485 ssdGkrrwgtvGvseniieasytallesieyklrkdeee 523
                                               + +Gk+ wgtvGvs niieas++al +++ y+l kde++
  lcl|NCBI__GCF_000215085.1:WP_013840437.1 490 TGNGKKTWGTVGVSTNIIEASWQALADGMAYGLLKDENN 528
                                               ************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (530 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: 11.38
//
[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