Alignments for a candidate for cimA in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Sulfurihydrogenibium subterraneum DSM 15120

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_028950471.1 Q385_RS0104225 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000619805.1:WP_028950471.1
          Length = 533

 Score =  611 bits (1575), Expect = e-179
 Identities = 296/517 (57%), Positives = 394/517 (76%), Gaps = 1/517 (0%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           V +YDTTLRDGTQAE +S  VEDK+RIA KL + G+HYIEGGWPGSNPKD+ FFK++KK 
Sbjct: 5   VLIYDTTLRDGTQAEGVSVSVEDKLRIAEKLADFGVHYIEGGWPGSNPKDMTFFKEVKKL 64

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
            L   KI AFGSTRR+ +  ++D  ++ LI+AE  V TIFGK+WD HV EAL+ +LE+NL
Sbjct: 65  NLKNTKITAFGSTRRSSLKVEEDPQIQDLIKAETPVITIFGKSWDLHVTEALKTTLEKNL 124

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
           E+I+DS+ YLK  V EV +DAEHFFDG+K NP+YA++ LK AQ A AD ++LCDTNGG++
Sbjct: 125 EMIYDSISYLKKYVDEVIFDAEHFFDGFKENPNYALEVLKVAQQAGADFLILCDTNGGSL 184

Query: 184 PFELVEIIREVRKH-ITAPLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNA 242
           P ++    + V++  ITA LGIH HNDS+ AV NS+ AV  G VQV GTING GERCGNA
Sbjct: 185 PTDIERAFKSVKEAGITAKLGIHAHNDSDTAVWNSIVAVLNGAVQVHGTINGIGERCGNA 244

Query: 243 NLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGGVH 302
           NLCSIIP L LK+  E +  + +++L+++S FV ++ N+   K+  YVG+SAFAHKGGVH
Sbjct: 245 NLCSIIPNLSLKLGYETVPRENIKRLKEISNFVSDIINMPVPKNMPYVGDSAFAHKGGVH 304

Query: 303 VSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEILEN 362
            SA+ R+P +YEH+ PE VGN  +VLVSDL+G+SNI+ KA+E  I++D KD    ++++ 
Sbjct: 305 ASAVLRNPRSYEHILPEEVGNRRKVLVSDLAGKSNIIYKAKEIGIEIDEKDERLTKLVQE 364

Query: 363 IKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLSEATIMVK 422
           IKE+EN+GY FE AEAS ELL+++ LGT  K+F +  +RV+  +R+ D+ P+SEAT+ +K
Sbjct: 365 IKELENQGYHFEAAEASLELLIRKHLGTLPKYFDLDAYRVLIARRYTDKSPISEATVRIK 424

Query: 423 VGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTASSIRVL 482
           +    EHTA+ G GPVNALD AL+KAL   YP L EV+L+DYKVR++    GTA+ IRVL
Sbjct: 425 IENHYEHTASLGYGPVNALDKALKKALTAVYPSLAEVELIDYKVRIVNESGGTAAKIRVL 484

Query: 483 IESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHK 519
           IES DK  +WGTVGVS+NI++AS+QA++DS+ YKL K
Sbjct: 485 IESRDKSKKWGTVGVSDNIIEASWQAVVDSIVYKLVK 521


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: 787
Number of extensions: 22
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: 533
Length adjustment: 35
Effective length of query: 493
Effective length of database: 498
Effective search space:   245514
Effective search space used:   245514
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_028950471.1 Q385_RS0104225 (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.31599.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-265  867.4   1.9   1.8e-265  867.1   1.9    1.0  1  lcl|NCBI__GCF_000619805.1:WP_028950471.1  Q385_RS0104225 citramalate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000619805.1:WP_028950471.1  Q385_RS0104225 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  867.1   1.9  1.8e-265  1.8e-265       2     520 ..       5     522 ..       4     526 .. 0.99

  Alignments for each domain:
  == domain 1  score: 867.1 bits;  conditional E-value: 1.8e-265
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               + +ydttlrdG+qaeGvs+s+edk+riaekl d+G+hyieGGwpg+npkd++ff++vk+ nlkn+k++a
  lcl|NCBI__GCF_000619805.1:WP_028950471.1   5 VLIYDTTLRDGTQAEGVSVSVEDKLRIAEKLADFGVHYIEGGWPGSNPKDMTFFKEVKKLNLKNTKITA 73 
                                               78******************************************************************* PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f+strr   kveed+q+q likaetpv+tifGkswdlhv+ealkttle+nl+miyd+++ylk+++devi
  lcl|NCBI__GCF_000619805.1:WP_028950471.1  74 FGSTRRSSLKVEEDPQIQDLIKAETPVITIFGKSWDLHVTEALKTTLEKNLEMIYDSISYLKKYVDEVI 142
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahnd 208
                                               +daehffdG+k np+yal++lkva++aGad+l+l+dtnGG+lp +ie   k vk+    ++lGihahnd
  lcl|NCBI__GCF_000619805.1:WP_028950471.1 143 FDAEHFFDGFKENPNYALEVLKVAQQAGADFLILCDTNGGSLPTDIERAFKSVKEAGITAKLGIHAHND 211
                                               ********************************************************************* PP

                                 TIGR00977 209 setavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvaei 277
                                               s+tav ns++av +Gavqv+GtinG+GercGnanlcs+ipnl lklg++ +++en+k+l e++++v++i
  lcl|NCBI__GCF_000619805.1:WP_028950471.1 212 SDTAVWNSIVAVLNGAVQVHGTINGIGERCGNANLCSIIPNLSLKLGYETVPRENIKRLKEISNFVSDI 280
                                               ********************************************************************* PP

                                 TIGR00977 278 vnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGi 346
                                               +n++ ++nmpyvG+safahkGGvh+sav rnp++yehi pe vGn+rk+ vs+laGksn++ k+ke+Gi
  lcl|NCBI__GCF_000619805.1:WP_028950471.1 281 INMPVPKNMPYVGDSAFAHKGGVHASAVLRNPRSYEHILPEEVGNRRKVLVSDLAGKSNIIYKAKEIGI 349
                                               ********************************************************************* PP

                                 TIGR00977 347 eidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdeeslsea 415
                                               eidek+ ++ k++++ikele+qGyhfeaaeaslell+r++lG+  kyf++d++rvlia+r  +   + +
  lcl|NCBI__GCF_000619805.1:WP_028950471.1 350 EIDEKDERLTKLVQEIKELENQGYHFEAAEASLELLIRKHLGTLPKYFDLDAYRVLIARRYTD-KSPIS 417
                                               **********************************************************99888.56889 PP

                                 TIGR00977 416 eatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvlie 484
                                               eatvr+ +e   e+ta++G Gpv+ald+al+kal+  ypsl++++l+dykvri+nes Gt ak+rvlie
  lcl|NCBI__GCF_000619805.1:WP_028950471.1 418 EATVRIKIENHYEHTASLGYGPVNALDKALKKALTAVYPSLAEVELIDYKVRIVNESGGTAAKIRVLIE 486
                                               9******************************************************************** PP

                                 TIGR00977 485 ssdGkrrwgtvGvseniieasytallesieyklrkd 520
                                               s d  ++wgtvGvs+niieas++a+++si+ykl kd
  lcl|NCBI__GCF_000619805.1:WP_028950471.1 487 SRDKSKKWGTVGVSDNIIEASWQAVVDSIVYKLVKD 522
                                               *********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (533 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: 11.00
//
[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