Alignments for a candidate for cimA in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Desulfobacter vibrioformis DSM 8776

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_035240746.1 Q366_RS15935 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000745975.1:WP_035240746.1
          Length = 544

 Score =  540 bits (1390), Expect = e-158
 Identities = 277/527 (52%), Positives = 364/527 (69%), Gaps = 5/527 (0%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           V LYDTTLRDG Q E+I F   DK++IA +LD+ GIHYIEGGWPGSNP   AFF  ++  
Sbjct: 10  VLLYDTTLRDGMQGENIFFSPGDKLKIAMRLDDAGIHYIEGGWPGSNPGAQAFFDLVRDT 69

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
              QAKI AFGSTRR   T +KD N+K LI +   V TIFGK+WD HV + +  + EENL
Sbjct: 70  PFKQAKICAFGSTRRQNSTCEKDSNIKALIDSGAPVVTIFGKSWDLHVSDIMNNTREENL 129

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
            +I +S+ YLKA   EV YDAEHF+DGYKANP +A++TL AA      C+VLCDTNGG +
Sbjct: 130 AMITESVSYLKARGREVLYDAEHFYDGYKANPGFALETLGAALKGGTRCLVLCDTNGGCL 189

Query: 184 PFELVEIIREVRKHIT----APLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERC 239
           P ++  I RE   H         G+HTHND   AVAN+++AV  G + VQGT+NG+GERC
Sbjct: 190 PCDIDTITRETIAHFKDYEDVIFGVHTHNDCAMAVANAINAVHAGAIMVQGTVNGYGERC 249

Query: 240 GNANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKG 299
           GNA+L ++IP L LKM R CI +  L KL++LSRFV E AN+ P   + +VG SAF HKG
Sbjct: 250 GNADLTALIPILALKMNRACISEKNLAKLQNLSRFVSETANMPPVASRPFVGRSAFTHKG 309

Query: 300 GVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEI 359
           GVHVSAI ++P  YEH+ PE VGN  RVLVS+ SG+SNI  KA+E  + + S +     I
Sbjct: 310 GVHVSAIMKNPRAYEHMSPEFVGNRRRVLVSEQSGKSNITYKAKELGVDLGSDESKKSLI 369

Query: 360 LENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLSEATI 419
           + NIKEMEN GY+F+ AE S +L+M+R    ++  F +  FRV+ EK  +++   S A I
Sbjct: 370 VNNIKEMENYGYEFDTAEGSLKLIMERLTEQYQSHFDLESFRVVVEK-DKERPCYSHAMI 428

Query: 420 MVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTASSI 479
            ++VG + E T+AEG+GPV+ALDNALRKAL   YP +K++ L+D+KVRV+    GT + +
Sbjct: 429 KIRVGNETEITSAEGDGPVSALDNALRKALTAMYPGVKDLHLVDFKVRVIDGSDGTDARV 488

Query: 480 RVLIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSEEIEGS 526
           RVLIES D+++ + TVGVS +I++AS+QAL DS +YKL      EG+
Sbjct: 489 RVLIESRDRDNIFSTVGVSADIIEASWQALADSFQYKLALDHAGEGN 535


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: 763
Number of extensions: 32
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: 528
Length of database: 544
Length adjustment: 35
Effective length of query: 493
Effective length of database: 509
Effective search space:   250937
Effective search space used:   250937
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_035240746.1 Q366_RS15935 (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.27502.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.4e-216  703.2   0.0   9.9e-216  703.0   0.0    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035240746.1  Q366_RS15935 citramalate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035240746.1  Q366_RS15935 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  703.0   0.0  9.9e-216  9.9e-216       1     523 [.       9     532 ..       9     535 .. 0.98

  Alignments for each domain:
  == domain 1  score: 703.0 bits;  conditional E-value: 9.9e-216
                                 TIGR00977   1 slklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvv 69 
                                               ++ lydttlrdG q e + +s  dk++ia +ldd GihyieGGwpg+np   aff  v++ ++k+ak++
  lcl|NCBI__GCF_000745975.1:WP_035240746.1   9 KVLLYDTTLRDGMQGENIFFSPGDKLKIAMRLDDAGIHYIEGGWPGSNPGAQAFFDLVRDTPFKQAKIC 77 
                                               5889***************************************************************** PP

                                 TIGR00977  70 afsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadev 138
                                               af+strr +   e+d++++ali++++pvvtifGkswdlhv + ++ t eenl+mi ++v+ylk  ++ev
  lcl|NCBI__GCF_000745975.1:WP_035240746.1  78 AFGSTRRQNSTCEKDSNIKALIDSGAPVVTIFGKSWDLHVSDIMNNTREENLAMITESVSYLKARGREV 146
                                               ********************************************************************* PP

                                 TIGR00977 139 iydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpq...lGih 204
                                               +ydaehf+dGykanp +al+tl +a k+G+ +lvl+dtnGG lp +i+ it++   ++kd +   +G+h
  lcl|NCBI__GCF_000745975.1:WP_035240746.1 147 LYDAEHFYDGYKANPGFALETLGAALKGGTRCLVLCDTNGGCLPCDIDTITRETIAHFKDYEdviFGVH 215
                                               *********************************************************976433338*** PP

                                 TIGR00977 205 ahndsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarl 273
                                               +hnd  +avan++ av+aGa +vqGt+nG+GercGna+l +lip l lk++  +i ++nl+kl +++r+
  lcl|NCBI__GCF_000745975.1:WP_035240746.1 216 THNDCAMAVANAINAVHAGAIMVQGTVNGYGERCGNADLTALIPILALKMNRACISEKNLAKLQNLSRF 284
                                               ********************************************************************* PP

                                 TIGR00977 274 vaeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklk 342
                                               v+e  n+++    p+vG+saf+hkGGvhvsa+ +np++yeh++pe+vGn+r++ vse++Gksn+  k+k
  lcl|NCBI__GCF_000745975.1:WP_035240746.1 285 VSETANMPPVASRPFVGRSAFTHKGGVHVSAIMKNPRAYEHMSPEFVGNRRRVLVSEQSGKSNITYKAK 353
                                               ********************************************************************* PP

                                 TIGR00977 343 elGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdees 411
                                               elG+++  ++ k   i+++ike+e+ Gy+f++ae sl+l++ +   + +++f++++frv+++k ++  +
  lcl|NCBI__GCF_000745975.1:WP_035240746.1 354 ELGVDLGSDESKKSLIVNNIKEMENYGYEFDTAEGSLKLIMERLTEQYQSHFDLESFRVVVEKDKERPC 422
                                               *******************************************************************9* PP

                                 TIGR00977 412 lseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktr 480
                                               +s+a++++rv +e+  e t aeG+Gpvsald+alrkal+ +yp +kdl+l+d+kvr++++s Gt+a++r
  lcl|NCBI__GCF_000745975.1:WP_035240746.1 423 YSHAMIKIRVGNET--EITSAEGDGPVSALDNALRKALTAMYPGVKDLHLVDFKVRVIDGSDGTDARVR 489
                                               ****9999998875..799************************************************** PP

                                 TIGR00977 481 vliessdGkrrwgtvGvseniieasytallesieyklrkdeee 523
                                               vlies d +  ++tvGvs +iieas++al +s +ykl +d+ +
  lcl|NCBI__GCF_000745975.1:WP_035240746.1 490 VLIESRDRDNIFSTVGVSADIIEASWQALADSFQYKLALDHAG 532
                                               *************************************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (544 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 7.38
//
[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