Alignments for a candidate for cimA in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Denitrovibrio acetiphilus DSM 12809

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_013010707.1 DACET_RS07115 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000025725.1:WP_013010707.1
          Length = 526

 Score =  674 bits (1739), Expect = 0.0
 Identities = 328/523 (62%), Positives = 407/523 (77%), Gaps = 3/523 (0%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           V++YDTTLRDGTQ+ED++F + DK++IA  L + G+ YIEGGWPGSNP+D+ FFK +K  
Sbjct: 5   VEIYDTTLRDGTQSEDVNFTIADKVKIAEALYDFGVRYIEGGWPGSNPRDIGFFKAVKGS 64

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
            +    IAAFGSTRRAK T D D N++ L++ E    TIFGKTWD HV EAL+I L++NL
Sbjct: 65  SVPDDHIAAFGSTRRAKRTCDNDENIQALLEVEVPNLTIFGKTWDLHVTEALKIELDQNL 124

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
           ELI DSL YLK  V   FYDAEHFFDGYKAN +YA++TLKAA DAKADCI+LCDTNGGTM
Sbjct: 125 ELINDSLSYLKTKVDRAFYDAEHFFDGYKANKEYALRTLKAAMDAKADCIILCDTNGGTM 184

Query: 184 PFELVEIIREVRKHITA--PLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGN 241
           P E+  II EVRK +T   PLGIH HNDS+CAVANS+ AV  GIV VQGT+NG+GERCGN
Sbjct: 185 PAEIGSIIDEVRK-VTGDYPLGIHCHNDSDCAVANSVIAVKHGIVHVQGTVNGYGERCGN 243

Query: 242 ANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGGV 301
           AN+ S+IP L+LK   EC+  D+L+ LR +SR++ EL NL  N HQ YVG SAFAHKGGV
Sbjct: 244 ANIMSVIPNLQLKYGYECVPVDKLKNLRTVSRYINELGNLKHNIHQPYVGRSAFAHKGGV 303

Query: 302 HVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEILE 361
           HVSAI ++  TYEH+ PELVGN  RVL+SDLSG+SN++ KA++F + +DS DP    ++E
Sbjct: 304 HVSAIMKNSSTYEHIEPELVGNRQRVLLSDLSGKSNLIYKAKDFGLDVDSSDPKINAVVE 363

Query: 362 NIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLSEATIMV 421
            +KE+EN+G+QFEGAEASFELLM++ +GT   FF  I +RVIDE       PL+EAT+M+
Sbjct: 364 RLKELENKGFQFEGAEASFELLMRKTMGTFTPFFDSISYRVIDEMNTNMGSPLAEATVMI 423

Query: 422 KVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTASSIRV 481
           KV G+ EHTAA GNGPVNA+DNA+RKAL  FYP LK+++L+DYKVR+L  G GT +  RV
Sbjct: 424 KVDGEQEHTAAAGNGPVNAIDNAIRKALLNFYPNLKDMELVDYKVRILTTGTGTEAVTRV 483

Query: 482 LIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSEEIE 524
           L+ES D +  WGTVGV+ NIVDASYQAL+DS+EYKL K +E E
Sbjct: 484 LVESKDTDGTWGTVGVATNIVDASYQALMDSIEYKLLKDKEKE 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: 902
Number of extensions: 30
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: 526
Length adjustment: 35
Effective length of query: 493
Effective length of database: 491
Effective search space:   242063
Effective search space used:   242063
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_013010707.1 DACET_RS07115 (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.14024.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-235  766.8   1.1   4.9e-235  766.7   1.1    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013010707.1  DACET_RS07115 citramalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013010707.1  DACET_RS07115 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  766.7   1.1  4.9e-235  4.9e-235       2     522 ..       5     524 ..       4     526 .] 0.99

  Alignments for each domain:
  == domain 1  score: 766.7 bits;  conditional E-value: 4.9e-235
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               + +ydttlrdG+q e v +++ dk++iae+l d+G++yieGGwpg+np+d+ ff++vk+ ++ + +++a
  lcl|NCBI__GCF_000025725.1:WP_013010707.1   5 VEIYDTTLRDGTQSEDVNFTIADKVKIAEALYDFGVRYIEGGWPGSNPRDIGFFKAVKGSSVPDDHIAA 73 
                                               78******************************************************************* PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f+strr ++  ++d+++qal++ e p +tifGk+wdlhv+ealk  l++nl++i d+++ylk  +d+  
  lcl|NCBI__GCF_000025725.1:WP_013010707.1  74 FGSTRRAKRTCDNDENIQALLEVEVPNLTIFGKTWDLHVTEALKIELDQNLELINDSLSYLKTKVDRAF 142
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahnd 208
                                               ydaehffdGykan+eyal+tlk+a +a ad+++l+dtnGGt+p ei  i+++v+k   d  lGih hnd
  lcl|NCBI__GCF_000025725.1:WP_013010707.1 143 YDAEHFFDGYKANKEYALRTLKAAMDAKADCIILCDTNGGTMPAEIGSIIDEVRKVTGDYPLGIHCHND 211
                                               ***********************************************************99******** PP

                                 TIGR00977 209 setavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvaei 277
                                               s+ avans++av+ G v+vqGt+nG+GercGnan+ s+ipnlqlk g+++++ ++lk+l  v+r++ e+
  lcl|NCBI__GCF_000025725.1:WP_013010707.1 212 SDCAVANSVIAVKHGIVHVQGTVNGYGERCGNANIMSVIPNLQLKYGYECVPVDKLKNLRTVSRYINEL 280
                                               ********************************************************************* PP

                                 TIGR00977 278 vnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGi 346
                                                nl ++ + pyvG+safahkGGvhvsa+ +n+ tyehi+pelvGn++++ +s+l+Gksn++ k+k++G+
  lcl|NCBI__GCF_000025725.1:WP_013010707.1 281 GNLKHNIHQPYVGRSAFAHKGGVHVSAIMKNSSTYEHIEPELVGNRQRVLLSDLSGKSNLIYKAKDFGL 349
                                               ********************************************************************* PP

                                 TIGR00977 347 eidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdeeslsea 415
                                               ++d ++pk++ +++++kele++G++fe+aeas+ell+r+++G+  ++f+  ++rv+ + +++    + a
  lcl|NCBI__GCF_000025725.1:WP_013010707.1 350 DVDSSDPKINAVVERLKELENKGFQFEGAEASFELLMRKTMGTFTPFFDSISYRVIDEMNTNM-GSPLA 417
                                               *******************************************************99999988.7799* PP

                                 TIGR00977 416 eatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvlie 484
                                               eatv + v+g +e+taa GnGpv+a+d+a+rkal +fyp+lkd++l+dykvril  ++Gt+a trvl+e
  lcl|NCBI__GCF_000025725.1:WP_013010707.1 418 EATVMIKVDGEQEHTAAAGNGPVNAIDNAIRKALLNFYPNLKDMELVDYKVRILTTGTGTEAVTRVLVE 486
                                               ********************************************************************* PP

                                 TIGR00977 485 ssdGkrrwgtvGvseniieasytallesieyklrkdee 522
                                               s d +  wgtvGv+ ni++asy+al++sieykl kd+e
  lcl|NCBI__GCF_000025725.1:WP_013010707.1 487 SKDTDGTWGTVGVATNIVDASYQALMDSIEYKLLKDKE 524
                                               ***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (526 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: 11.22
//
[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