Alignments for a candidate for cysK in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Desulfotalea psychrophila LSv54

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_011188481.1 DP_RS06260 cysteine synthase A

Query= BRENDA::P9WP55
         (310 letters)



>NCBI__GCF_000025945.1:WP_011188481.1
          Length = 306

 Score =  343 bits (880), Expect = 3e-99
 Identities = 179/300 (59%), Positives = 218/300 (72%)

Query: 7   ITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIKPDTI 66
           I Q IG TPL++L R+     A I+ K E  NPA SVK R+ V+M++   + G I   T 
Sbjct: 5   IGQSIGNTPLLKLGRLDRDCAATILVKQESRNPAGSVKCRVAVSMIETGLREGKISKGTT 64

Query: 67  ILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGADGMSGAI 126
           I+EPTSGNTGI LA VCAA+G R +LTMPE+MS+ERR LL   GAE++LTP A+GM+GAI
Sbjct: 65  IVEPTSGNTGIGLAFVCAAKGLRLILTMPESMSIERRKLLAHLGAEIVLTPAAEGMTGAI 124

Query: 127 AKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGTITGV 186
            KAEEL       F+P QF NPANP IHR TT +E+ RDTDG+VDI VAGVGTGGT+TGV
Sbjct: 125 TKAEELLTGLADGFMPDQFNNPANPEIHRQTTGKEILRDTDGRVDIFVAGVGTGGTLTGV 184

Query: 187 AQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIITVGNE 246
             V+K + P  + +AVEPA S V+SG   GPH IQGIGAGF+P  LD  L+DE I V +E
Sbjct: 185 GSVLKAKNPRVQVIAVEPATSAVISGEAPGPHGIQGIGAGFIPGNLDISLIDETIKVNDE 244

Query: 247 DALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYLSTPLFA 306
           DAL  A+ LA +EG+L GISSGAA  A+L+VA+RPEN GK IV +LPD GERYLST LF+
Sbjct: 245 DALVAAQELATQEGILCGISSGAAFWASLEVAKRPENIGKTIVTILPDTGERYLSTNLFS 304


Lambda     K      H
   0.318    0.136    0.383 

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: 335
Number of extensions: 17
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: 310
Length of database: 306
Length adjustment: 27
Effective length of query: 283
Effective length of database: 279
Effective search space:    78957
Effective search space used:    78957
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_011188481.1 DP_RS06260 (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.7249.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-137  441.8   0.6   6.6e-137  441.6   0.6    1.0  1  lcl|NCBI__GCF_000025945.1:WP_011188481.1  DP_RS06260 cysteine synthase A


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025945.1:WP_011188481.1  DP_RS06260 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.6   0.6  6.6e-137  6.6e-137       3     298 .]       7     303 ..       5     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 441.6 bits;  conditional E-value: 6.6e-137
                                 TIGR01139   3 eliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGi 70 
                                               + iGntPl++L  l  +++a +lvk es+nP++svk+r+a++mie   +eg++ kg+tive+tsGntGi
  lcl|NCBI__GCF_000025945.1:WP_011188481.1   7 QSIGNTPLLKLGrLDRDCAATILVKQESRNPAGSVKCRVAVSMIETGLREGKISKGTTIVEPTSGNTGI 75 
                                               78*********98999***************************************************** PP

                                 TIGR01139  71 alamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqf 139
                                               +la+v+aa+g++liltmpe+ms+errkll  +Gae+vLt++aegm+gai+kaeel++  ++ + ++ qf
  lcl|NCBI__GCF_000025945.1:WP_011188481.1  76 GLAFVCAAKGLRLILTMPESMSIERRKLLAHLGAEIVLTPAAEGMTGAITKAEELLTGLADGF-MPDQF 143
                                               ************************************************************999.***** PP

                                 TIGR01139 140 enpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggk 208
                                               +npanpeihr+tt++eil+d+dg++d+fvagvGtGGt+tGvg+vlk k+p ++v+avePa+s+v+sg+ 
  lcl|NCBI__GCF_000025945.1:WP_011188481.1 144 NNPANPEIHRQTTGKEILRDTDGRVDIFVAGVGTGGTLTGVGSVLKAKNPRVQVIAVEPATSAVISGEA 212
                                               ********************************************************************* PP

                                 TIGR01139 209 pgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle. 276
                                               pgph iqGigagfiP +Ld ++ide ikv+de+a+  a++la++eGil GissGaa +a+l+vak++e 
  lcl|NCBI__GCF_000025945.1:WP_011188481.1 213 PGPHGIQGIGAGFIPGNLDISLIDETIKVNDEDALVAAQELATQEGILCGISSGAAFWASLEVAKRPEn 281
                                               ********************************************************************9 PP

                                 TIGR01139 277 kdkkivvilpdtgerYlstaLf 298
                                                +k+iv+ilpdtgerYlst+Lf
  lcl|NCBI__GCF_000025945.1:WP_011188481.1 282 IGKTIVTILPDTGERYLSTNLF 303
                                               9********************9 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.97
//
[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