Alignments for a candidate for cysK in Trichodesmium erythraeum IMS101

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Trichodesmium erythraeum IMS101

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_011610965.1 TERY_RS05770 cysteine synthase A

Query= BRENDA::A8YBS4
         (319 letters)



>NCBI__GCF_000014265.1:WP_011610965.1
          Length = 320

 Score =  475 bits (1223), Expect = e-139
 Identities = 235/312 (75%), Positives = 274/312 (87%), Gaps = 1/312 (0%)

Query: 1   MRIAHDVTELVGRTPLVQLNRIPQAEGCLGRIVMKLEGMNPAASVKDRIGTHMINSAEKA 60
           MRIAH++TELVGRTPLVQLN IP+AEGCL +I++KLEGMNPAASVKDRIG +MIN AE+ 
Sbjct: 1   MRIAHNITELVGRTPLVQLNSIPKAEGCLAKIIVKLEGMNPAASVKDRIGVNMINVAERE 60

Query: 61  GLINPETTVLVEPTSGNTGIALAMTAAAKGYRLILTMPETMSLERRAMLKAYGATLELTP 120
           GLI P  T LVEPTSGNTGIALAM AAA+GY+LILTMPETMS+ERR ML+AYGA L LTP
Sbjct: 61  GLIKPGKTTLVEPTSGNTGIALAMVAAARGYKLILTMPETMSMERRVMLRAYGAELVLTP 120

Query: 121 GSQGMKGAILRAQQIVD-SIPGAYMLQQFRNPSNPEIHRLTTAEEIWQDTEGQVDFIVAG 179
           GS+GMKGAI +AQ+IVD S  G YMLQQF+NP+NPEIH  TTA EIW+DT+G+VD +VAG
Sbjct: 121 GSEGMKGAITKAQEIVDLSSNGYYMLQQFQNPANPEIHSKTTALEIWEDTDGKVDILVAG 180

Query: 180 VGTGGTITGVAEVIKSRKPSFQVVAVEPFNSPVISGGNPGPHKIQGIGAGFIPEVLRTDL 239
           VGTGGT+TGVAE IK+RKP FQ +AVEP NSPV+SGG PGPHKIQGIGAGF+P+VL T +
Sbjct: 181 VGTGGTVTGVAETIKARKPEFQAIAVEPSNSPVLSGGKPGPHKIQGIGAGFVPDVLDTKI 240

Query: 240 IDEVITVSDEEAFQFGRRLAKEEGLLSGISSGANLCAAIQLAQRPENEGKLIVVIQPSFG 299
           IDEVI V D EA  +GRR+AKEEG+LSGIS+GA LCAAI++ +RPEN+GKLIV+IQPSFG
Sbjct: 241 IDEVIQVPDSEAMVYGRRIAKEEGILSGISTGAALCAAIEVGKRPENDGKLIVMIQPSFG 300

Query: 300 ERYLSTLMFQNI 311
           ERYLST +FQ +
Sbjct: 301 ERYLSTPLFQEL 312


Lambda     K      H
   0.317    0.135    0.378 

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: 424
Number of extensions: 9
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: 319
Length of database: 320
Length adjustment: 28
Effective length of query: 291
Effective length of database: 292
Effective search space:    84972
Effective search space used:    84972
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_011610965.1 TERY_RS05770 (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.27510.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-147  475.0   1.3     5e-147  474.9   1.3    1.0  1  lcl|NCBI__GCF_000014265.1:WP_011610965.1  TERY_RS05770 cysteine synthase A


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011610965.1  TERY_RS05770 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.9   1.3    5e-147    5e-147       1     298 []       7     309 ..       7     309 .. 0.99

  Alignments for each domain:
  == domain 1  score: 474.9 bits;  conditional E-value: 5e-147
                                 TIGR01139   1 iseliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgk.tiveats 65 
                                               i+el+G+tPlv+Ln    ae++ a+++vkle +nP++svkdri+++mi+ ae+egl+k+gk t+ve+ts
  lcl|NCBI__GCF_000014265.1:WP_011610965.1   7 ITELVGRTPLVQLNsipKAEGCLAKIIVKLEGMNPAASVKDRIGVNMINVAEREGLIKPGKtTLVEPTS 75 
                                               689***********877789999*************************************989****** PP

                                 TIGR01139  66 GntGialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkyl 134
                                               GntGialamvaaargykliltmpetms+err +l+ayGaelvLt+g+egmkgai+ka+e+v+ ++n y+
  lcl|NCBI__GCF_000014265.1:WP_011610965.1  76 GNTGIALAMVAAARGYKLILTMPETMSMERRVMLRAYGAELVLTPGSEGMKGAITKAQEIVDLSSNGYY 144
                                               ********************************************************************* PP

                                 TIGR01139 135 llkqfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespv 203
                                               +l+qf+npanpeih ktta ei++d+dgk+d++vagvGtGGt+tGv+e++k  kp+++++aveP++spv
  lcl|NCBI__GCF_000014265.1:WP_011610965.1 145 MLQQFQNPANPEIHSKTTALEIWEDTDGKVDILVAGVGTGGTVTGVAETIKARKPEFQAIAVEPSNSPV 213
                                               ********************************************************************* PP

                                 TIGR01139 204 lsggkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkva 272
                                               lsggkpgphkiqGigagf+P+vLd+++idevi+v d ea+ ++rr+akeeGil+Gis+Gaa+ aa++v 
  lcl|NCBI__GCF_000014265.1:WP_011610965.1 214 LSGGKPGPHKIQGIGAGFVPDVLDTKIIDEVIQVPDSEAMVYGRRIAKEEGILSGISTGAALCAAIEVG 282
                                               ********************************************************************* PP

                                 TIGR01139 273 kkle.kdkkivvilpdtgerYlstaLf 298
                                               k++e ++k+iv+i+p++gerYlst+Lf
  lcl|NCBI__GCF_000014265.1:WP_011610965.1 283 KRPEnDGKLIVMIQPSFGERYLSTPLF 309
                                               ****899*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (320 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: 00:00:00.01
# Mc/sec: 9.35
//
[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