Alignments for a candidate for cimA in Rhodopseudomonas palustris CGA009

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Rhodopseudomonas palustris CGA009

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_011157555.1 TX73_RS10200 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000195775.1:WP_011157555.1
          Length = 532

 Score =  468 bits (1204), Expect = e-136
 Identities = 260/525 (49%), Positives = 342/525 (65%), Gaps = 14/525 (2%)

Query: 6   LYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKEKL 65
           LYDTTLRDG Q   + F + DK  IA  LD++GI Y+EGG+PG+NP D  FF    ++KL
Sbjct: 8   LYDTTLRDGAQTNGVDFTLHDKKLIASLLDDLGIDYVEGGYPGANPLDTEFFGT--EQKL 65

Query: 66  SQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENLEL 125
            +A  AAFG TRR   +   D  +  LI A+ D      K+ ++ V  AL  + EEN+  
Sbjct: 66  ERATFAAFGMTRRPGRSASNDPGIAMLIDAKADAICFVAKSSEYQVRVALETTNEENIAS 125

Query: 126 IFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTMPF 185
           I DS+   K    EV  D EHFFDGYKANP++A++  KAA ++ A  +VLCDTNGGTMP 
Sbjct: 126 IRDSVSLAKDKGREVLVDCEHFFDGYKANPEFALQCAKAAYESGARWVVLCDTNGGTMPD 185

Query: 186 ELVEIIREVRKHIT-APLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNANL 244
           E+  I+ EV KHI  A +GIH HND+E AVANS  AV  G  Q+QGT+NG GERCGNANL
Sbjct: 186 EVEAIVGEVVKHIPGAHVGIHAHNDTEQAVANSFAAVRAGARQIQGTLNGLGERCGNANL 245

Query: 245 CSIIPALKLKMK-----RECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKG 299
           CS+IP LKLK +        + DD+L  L  +SR +  + + +PN H  YVG SAF  K 
Sbjct: 246 CSMIPTLKLKKEFADKFEIGVSDDKLASLVQVSRALDNILDRAPNPHAPYVGGSAFVTKT 305

Query: 300 GVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEI 359
           G+H SA+ + P+TYEH+ PE +GN  +VLVSD +G+SN+LA+    NI+ D  DP    +
Sbjct: 306 GIHASAVLKDPQTYEHVPPESIGNHRKVLVSDQAGKSNVLAELARTNIQFDRDDPRLSRL 365

Query: 360 LENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKR---HEDQKPLSE 416
           +E +KE E  GY +E A ASF+LL +  LGT  +FF V  F V  E+R   H  +  ++ 
Sbjct: 366 VEKLKEREAAGYAYESANASFDLLARSTLGTVPEFFRVDKFDVNVEQRYNSHGQRVTVAM 425

Query: 417 ATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTA 476
           A I V+V G+   +AAEGNGPVNALD ALRK L K+   ++ +KL+DY+VR+L    GT 
Sbjct: 426 AVIKVEVDGETLISAAEGNGPVNALDVALRKDLGKYQKYIEGLKLVDYRVRIL--NGGTE 483

Query: 477 SSIRVLIESGDKES-RWGTVGVSENIVDASYQALLDSVEYKLHKS 520
           +  RVLIES D++  RW T+GVS NI+DAS+QAL+DSV YKL +S
Sbjct: 484 AVTRVLIESEDEDGRRWTTIGVSPNIIDASFQALMDSVVYKLVQS 528


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: 732
Number of extensions: 29
Number of successful extensions: 7
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: 532
Length adjustment: 35
Effective length of query: 493
Effective length of database: 497
Effective search space:   245021
Effective search space used:   245021
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_011157555.1 TX73_RS10200 (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.14632.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-192  625.1   0.1   4.9e-192  624.8   0.1    1.0  1  lcl|NCBI__GCF_000195775.1:WP_011157555.1  TX73_RS10200 citramalate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195775.1:WP_011157555.1  TX73_RS10200 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  624.8   0.1  4.9e-192  4.9e-192       2     520 ..       6     528 ..       5     531 .. 0.97

  Alignments for each domain:
  == domain 1  score: 624.8 bits;  conditional E-value: 4.9e-192
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               l+lydttlrdGaq++Gv ++l+dk  ia  lddlGi+y+eGG+pganp d++ff    e++l++a  +a
  lcl|NCBI__GCF_000195775.1:WP_011157555.1   6 LYLYDTTLRDGAQTNGVDFTLHDKKLIASLLDDLGIDYVEGGYPGANPLDTEFFGT--EQKLERATFAA 72 
                                               89****************************************************87..55799****** PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f+ trrp +  ++d+ +  li+a++  +    ks +  v  al+tt een++ i d+v+  k  ++ev+
  lcl|NCBI__GCF_000195775.1:WP_011157555.1  73 FGMTRRPGRSASNDPGIAMLIDAKADAICFVAKSSEYQVRVALETTNEENIASIRDSVSLAKDKGREVL 141
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahnd 208
                                                d ehffdGykanpe+al+  k+a ++Ga w+vl+dtnGGt+p+e+e i+ +v k++  +++Gihahnd
  lcl|NCBI__GCF_000195775.1:WP_011157555.1 142 VDCEHFFDGYKANPEFALQCAKAAYESGARWVVLCDTNGGTMPDEVEAIVGEVVKHIPGAHVGIHAHND 210
                                               ********************************************************************* PP

                                 TIGR00977 209 setavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgld....v.iekenlkkltevar 272
                                               +e avans++av+aGa+q+qGt+nGlGercGnanlcs+ip l+lk ++     + + +++l+ l++v+r
  lcl|NCBI__GCF_000195775.1:WP_011157555.1 211 TEQAVANSFAAVRAGARQIQGTLNGLGERCGNANLCSMIPTLKLKKEFAdkfeIgVSDDKLASLVQVSR 279
                                               *********************************************9874222244789*********** PP

                                 TIGR00977 273 lvaeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvlekl 341
                                                + +i ++a++ ++pyvG saf  k G+h+sav ++p+tyeh+ pe +Gn+rk+ vs++aGksnvl  l
  lcl|NCBI__GCF_000195775.1:WP_011157555.1 280 ALDNILDRAPNPHAPYVGGSAFVTKTGIHASAVLKDPQTYEHVPPESIGNHRKVLVSDQAGKSNVLAEL 348
                                               ********************************************************************* PP

                                 TIGR00977 342 kelGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdee 410
                                                   i++d+++p++ ++++k+ke e+ Gy +e+a+as++ll r++lG++ ++f vd f v +++r +  
  lcl|NCBI__GCF_000195775.1:WP_011157555.1 349 ARTNIQFDRDDPRLSRLVEKLKEREAAGYAYESANASFDLLARSTLGTVPEFFRVDKFDVNVEQRYNSH 417
                                               ***************************************************************998887 PP

                                 TIGR00977 411 ..slseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsa 477
                                                  ++ a+a ++v v+g     aaeGnGpv+ald alrk l k+   ++ lkl+dy+vriln+  Gt+a
  lcl|NCBI__GCF_000195775.1:WP_011157555.1 418 gqRVTVAMAVIKVEVDGETLISAAEGNGPVNALDVALRKDLGKYQKYIEGLKLVDYRVRILNG--GTEA 484
                                               4467789999***************************************************97..9*** PP

                                 TIGR00977 478 ktrvliessdGk.rrwgtvGvseniieasytallesieyklrkd 520
                                                trvlies d + rrw+t+Gvs+nii+as++al++s++ykl + 
  lcl|NCBI__GCF_000195775.1:WP_011157555.1 485 VTRVLIESEDEDgRRWTTIGVSPNIIDASFQALMDSVVYKLVQS 528
                                               ********997659***************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (532 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: 00:00:00.03
# Mc/sec: 8.95
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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