Alignments for a candidate for cysK in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Malonomonas rubra DSM 5091

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_072907665.1 BUB13_RS08065 cysteine synthase A

Query= BRENDA::E5LPF4
         (309 letters)



>NCBI__GCF_900142125.1:WP_072907665.1
          Length = 306

 Score =  338 bits (868), Expect = 7e-98
 Identities = 173/303 (57%), Positives = 221/303 (72%), Gaps = 1/303 (0%)

Query: 3   TAADNITGLIGNTPLLKLNRVVPEDAADVYVKLEFFNPGGSVKDRIALAMIEDAEYKGVL 62
           T + ++   IGN+PL+KL+       A V+ KLE  NPGGS+KDRIALAM+EDAE KG+L
Sbjct: 4   TTSSSLLDQIGNSPLVKLSAFSQPGKATVWGKLESSNPGGSIKDRIALAMVEDAESKGLL 63

Query: 63  KPGGTIVEPTSGNTGIGLALVAAAKGYHLIITMPETMSVERRALMRGYGAELILTPGADG 122
            PG TIVEPTSGNTGIGLA++AA KGY LI+TMPETMS ER  L   YGAEL+LTPG+ G
Sbjct: 64  SPGMTIVEPTSGNTGIGLAMIAAIKGYKLILTMPETMSQERCRLFTSYGAELVLTPGSQG 123

Query: 123 MPGAIKKAQALSKENGYFLPMQFQNPANPDVHERTTGQEIIRSFDGGTPDAFVAGVGTGG 182
           M GAIKKA  +++    F+P QF NPANP +HE+TTG EII + +G   D FVAGVGTGG
Sbjct: 124 MRGAIKKATEIAQTKAAFMPQQFCNPANPAIHEKTTGPEIIAALEGKV-DMFVAGVGTGG 182

Query: 183 TLTGVGRALRKINPQVQIYALEAAESPMLKEGHGGKHKIQGISAGFIPDVLDTNLYQDII 242
           T+TGVG  LR+ N  V+I A+E + S  L  G  G H IQGI AGF+PD+LD ++Y  ++
Sbjct: 183 TITGVGHCLRQHNAAVKIVAVEPSNSATLSGGDAGPHAIQGIGAGFVPDILDQDVYDQVV 242

Query: 243 EVTSDQAIDMARHVSHEEGFLPGISAGANIFGAIEIAKKLGKGKSVVTVAPDNGERYLST 302
            V+   AI M R+++ +EG L GISAGAN+F A E+A K+ +G++VVT+  D GERYLST
Sbjct: 243 TVSDADAIRMTRNLAVKEGLLCGISAGANVFVASELAAKMDEGQNVVTIICDTGERYLST 302

Query: 303 DLF 305
            ++
Sbjct: 303 GIY 305


Lambda     K      H
   0.316    0.137    0.390 

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: 325
Number of extensions: 10
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: 309
Length of database: 306
Length adjustment: 27
Effective length of query: 282
Effective length of database: 279
Effective search space:    78678
Effective search space used:    78678
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_072907665.1 BUB13_RS08065 (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.3153929.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-134  432.4   1.0     5e-134  432.2   1.0    1.0  1  NCBI__GCF_900142125.1:WP_072907665.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900142125.1:WP_072907665.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.2   1.0    5e-134    5e-134       3     298 .]      11     305 ..       9     305 .. 0.98

  Alignments for each domain:
  == domain 1  score: 432.2 bits;  conditional E-value: 5e-134
                             TIGR01139   3 eliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialam 74 
                                           + iGn Plv+L    ++ ka v  kles nP++s+kdrialam+edae +gll +g tive+tsGntGi+lam
  NCBI__GCF_900142125.1:WP_072907665.1  11 DQIGNSPLVKLSaFSQPGKATVWGKLESSNPGGSIKDRIALAMVEDAESKGLLSPGMTIVEPTSGNTGIGLAM 83 
                                           67**********888999******************************************************* PP

                             TIGR01139  75 vaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpei 147
                                           +aa +gykliltmpetms+er +l+++yGaelvLt+g++gm+gai+ka e++++++   ++++qf npanp+i
  NCBI__GCF_900142125.1:WP_072907665.1  84 IAAIKGYKLILTMPETMSQERCRLFTSYGAELVLTPGSQGMRGAIKKATEIAQTKA--AFMPQQFCNPANPAI 154
                                           ****************************************************9998..55************* PP

                             TIGR01139 148 hrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGigag 220
                                           h+ktt+pei+ +l+gk+d+fvagvGtGGtitGvg+ l+++++ +k+vaveP++s+ lsgg++gph+iqGigag
  NCBI__GCF_900142125.1:WP_072907665.1 155 HEKTTGPEIIAALEGKVDMFVAGVGTGGTITGVGHCLRQHNAAVKIVAVEPSNSATLSGGDAGPHAIQGIGAG 227
                                           ************************************************************************* PP

                             TIGR01139 221 fiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakklekdkkivvilpdtgerYl 293
                                           f+P++Ld++v+d+v++vsd +ai+++r+la +eG+l Gis+Ga+v+ a ++a k+++++++v+i++dtgerYl
  NCBI__GCF_900142125.1:WP_072907665.1 228 FVPDILDQDVYDQVVTVSDADAIRMTRNLAVKEGLLCGISAGANVFVASELAAKMDEGQNVVTIICDTGERYL 300
                                           ************************************************************************* PP

                             TIGR01139 294 staLf 298
                                           st ++
  NCBI__GCF_900142125.1:WP_072907665.1 301 STGIY 305
                                           **876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (306 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.12
//
[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:

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