GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Desulforamulus 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.419260.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  NCBI__GCF_000215085.1:WP_013840437.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013840437.1  
   #    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 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 
                                           +k+ydt+lrdG+q eGvsls edk++ia++ld++G hyieGGwpg+npkd++ff ++++ +lkna v+af+st
  NCBI__GCF_000215085.1:WP_013840437.1  11 IKIYDTSLRDGTQGEGVSLSAEDKMKIARRLDEMGFHYIEGGWPGSNPKDMEFFARLRQTPLKNALVTAFGST 83 
                                           79*********************************************************************** PP

                             TIGR00977  75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147
                                            rp ++   d++l+ l++++ +  +ifGk+wd+hv++al+t+leenl+m+ d+v+ylk+++  v +d ehffd
  NCBI__GCF_000215085.1:WP_013840437.1  84 CRPGVEAARDENLNRLLESGVRAAAIFGKTWDFHVTKALNTSLEENLRMVRDSVAYLKQQGLTVFFDGEHFFD 156
                                           ************************************************************************* PP

                             TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllav 220
                                           G+kanp+yal +l++a ++Gad +vl+dtnGGtlphe++ ++ +vk++l   +lGihahnd e+avan+++av
  NCBI__GCF_000215085.1:WP_013840437.1 157 GFKANPDYALSVLRAAVEGGADAVVLCDTNGGTLPHELQSVVARVKQELPGVELGIHAHNDGEMAVANTIVAV 229
                                           ************************************************************************* PP

                             TIGR00977 221 eaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvaeivnlaldenmpyvGesa 293
                                           +aG +qvqGt+nGlGercGnanlcs++pnl lklg++ i++en++ lte++r+v e+ nl + +n p+vGesa
  NCBI__GCF_000215085.1:WP_013840437.1 230 QAGVTQVQGTVNGLGERCGNANLCSILPNLTLKLGYETIPRENFAFLTELSRFVYEVANLNPVNNQPFVGESA 302
                                           ************************************************************************* PP

                             TIGR00977 294 fahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikele 366
                                           fahkGG+hvsa+ ++p tyeh+ pe vGn r++ +sel+G+sn+l k kel  ++d++sp+ r++l+++k++e
  NCBI__GCF_000215085.1:WP_013840437.1 303 FAHKGGIHVSALLKEPGTYEHMPPEWVGNTRRVLMSELSGLSNLLYKYKEL--HLDKSSPEGRRVLEQLKNME 373
                                           *************************************************96..79****************** PP

                             TIGR00977 367 kqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdeeslseaeatvrvsvegaeeltaaeGnGpvs 439
                                           ++Gy+feaae sle+++r+a+   ++ f+++++r++++ r d    sea +++rv +e+  ++taaeGnGpv+
  NCBI__GCF_000215085.1:WP_013840437.1 374 HRGYQFEAAEGSLEIMLRKAVNGYREPFQLESMRLILEMREDRPIQSEAVIKLRVGEEV--VHTAAEGNGPVN 444
                                           *************************************9999998888888888888887..59********** PP

                             TIGR00977 440 aldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGkrrwgtvGvseniieasytalles 512
                                           ald+alrkale  yp++  l+l+dykvr+l+e+aGt+a++rvlie+ +Gk+ wgtvGvs niieas++al ++
  NCBI__GCF_000215085.1:WP_013840437.1 445 ALDNALRKALETVYPEVPGLRLLDYKVRVLEEKAGTEAQVRVLIETGNGKKTWGTVGVSTNIIEASWQALADG 517
                                           ************************************************************************* PP

                             TIGR00977 513 ieyklrkdeee 523
                                           + y+l kde++
  NCBI__GCF_000215085.1:WP_013840437.1 518 MAYGLLKDENN 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 33.34
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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