Alignments for a candidate for cysK in Rhodospirillum centenum SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Rhodospirillum centenum SW; ATCC 51521

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_012568193.1 RC1_RS14565 cysteine synthase A

Query= BRENDA::Q2PZM5
         (319 letters)



>NCBI__GCF_000016185.1:WP_012568193.1
          Length = 333

 Score =  490 bits (1261), Expect = e-143
 Identities = 250/316 (79%), Positives = 278/316 (87%)

Query: 4   SEFRGKIYDSILDTVGATPLVRVNRLAEDAGAKAQIVGKLEFFNPLASVKDRIGFAMIDA 63
           +EFRG+IYDSILDTVGATPLVR++RLA   G  A +V K EFFNPL+SVKDRIG AMI+A
Sbjct: 18  AEFRGRIYDSILDTVGATPLVRLSRLAAKHGVVADVVAKCEFFNPLSSVKDRIGKAMIEA 77

Query: 64  AERAGTIEPGRTTLVEPTSGNTGIALAFVAAAKGYRLILTMPESMSVERRKMLKLLGAEL 123
           AE  G I P RT LVEPTSGNTGIALAFVAAAKGYRLILTMPESMSVERRKMLKLLGAEL
Sbjct: 78  AEADGLIAPDRTVLVEPTSGNTGIALAFVAAAKGYRLILTMPESMSVERRKMLKLLGAEL 137

Query: 124 VLTPAAEGMKGAIRRADEIVATDPNAYMLQQFKNAANPEIHRNTTAEEIWKDTDGKADFL 183
           VLTPA  GMKGAI RA+EIVA+ P+AYMLQQFKN ANP +HR TTAEEIW+DT G+AD L
Sbjct: 138 VLTPAPNGMKGAIARAEEIVASTPDAYMLQQFKNPANPAVHRRTTAEEIWRDTAGRADVL 197

Query: 184 ISGVGTGGTLTGVSEVLKARKPGFRTIAVEPEDSPVLSGGMPGPHKIQGIGAGFVPDVLK 243
           ++GVGTGGTLTGV+EVLKAR+P FR +AVEPEDSPVLSGG+PGPHKIQGIGAGFVPDVL 
Sbjct: 198 VAGVGTGGTLTGVAEVLKARRPDFRVVAVEPEDSPVLSGGLPGPHKIQGIGAGFVPDVLA 257

Query: 244 KDLIDEVVRISNQRAFETARKVAKLEGIPVGISSGAALAAALEIGSRPENEGKLIVVILP 303
           +D IDEV+RISN RAFE AR  A  EG+ VGISSGAALAAA E+G+RPE + +LIVVILP
Sbjct: 258 RDRIDEVLRISNSRAFELARDAAATEGLAVGISSGAALAAAFEVGARPEMKDRLIVVILP 317

Query: 304 SFAERYLSTALFEGLE 319
           SFAERYLSTALF+GL+
Sbjct: 318 SFAERYLSTALFDGLD 333


Lambda     K      H
   0.316    0.135    0.376 

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: 383
Number of extensions: 8
Number of successful extensions: 1
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: 319
Length of database: 333
Length adjustment: 28
Effective length of query: 291
Effective length of database: 305
Effective search space:    88755
Effective search space used:    88755
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: 48 (23.1 bits)

Align candidate WP_012568193.1 RC1_RS14565 (cysteine synthase A)
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))

# 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/TIGR01139.hmm
# target sequence database:        /tmp/gapView.21950.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01139  [M=298]
Accession:   TIGR01139
Description: cysK: cysteine synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-135  436.3   0.0   3.1e-135  436.1   0.0    1.0  1  lcl|NCBI__GCF_000016185.1:WP_012568193.1  RC1_RS14565 cysteine synthase A


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016185.1:WP_012568193.1  RC1_RS14565 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.1   0.0  3.1e-135  3.1e-135       2     298 .]      29     329 ..      28     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 436.1 bits;  conditional E-value: 3.1e-135
                                 TIGR01139   2 seliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgk.tiveatsG 66 
                                                +++G tPlvrL     ++++ a+v++k+e++nP ssvkdri+ amie ae +gl+ +++ ++ve+tsG
  lcl|NCBI__GCF_000016185.1:WP_012568193.1  29 LDTVGATPLVRLSrlaAKHGVVADVVAKCEFFNPLSSVKDRIGKAMIEAAEADGLIAPDRtVLVEPTSG 97 
                                               579*********97444567789***********************************98689****** PP

                                 TIGR01139  67 ntGialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkyll 135
                                               ntGiala+vaaa+gy+liltmpe+ms+errk+lk +GaelvLt++ +gmkgai++aee+v++tp++y +
  lcl|NCBI__GCF_000016185.1:WP_012568193.1  98 NTGIALAFVAAAKGYRLILTMPESMSVERRKMLKLLGAELVLTPAPNGMKGAIARAEEIVASTPDAY-M 165
                                               *******************************************************************.* PP

                                 TIGR01139 136 lkqfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvl 204
                                               l+qf+npanp++hr+tta+ei++d+ g+ d++vagvGtGGt+tGv+evlk  +pd++vvaveP++spvl
  lcl|NCBI__GCF_000016185.1:WP_012568193.1 166 LQQFKNPANPAVHRRTTAEEIWRDTAGRADVLVAGVGTGGTLTGVAEVLKARRPDFRVVAVEPEDSPVL 234
                                               ********************************************************************* PP

                                 TIGR01139 205 sggkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvak 273
                                               sgg pgphkiqGigagf+P+vL ++ idev+++s+  a+e+ar  a+ eG+ vGissGaa+aaa +v  
  lcl|NCBI__GCF_000016185.1:WP_012568193.1 235 SGGLPGPHKIQGIGAGFVPDVLARDRIDEVLRISNSRAFELARDAAATEGLAVGISSGAALAAAFEVGA 303
                                               ********************************************************************* PP

                                 TIGR01139 274 kle.kdkkivvilpdtgerYlstaLf 298
                                               ++e kd++ivvilp+++erYlstaLf
  lcl|NCBI__GCF_000016185.1:WP_012568193.1 304 RPEmKDRLIVVILPSFAERYLSTALF 329
                                               *999*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (333 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.16
//
[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