Alignments for a candidate for cysK in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Halorhodospira halophila SL1

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_041595022.1 HHAL_RS02830 cysteine synthase A

Query= BRENDA::Q2PZM5
         (319 letters)



>NCBI__GCF_000015585.1:WP_041595022.1
          Length = 326

 Score =  385 bits (988), Expect = e-111
 Identities = 191/312 (61%), Positives = 240/312 (76%)

Query: 8   GKIYDSILDTVGATPLVRVNRLAEDAGAKAQIVGKLEFFNPLASVKDRIGFAMIDAAERA 67
           G+IYD  + T+G TPLVR++RL  +AG  A+++ KLE FNPL+SVKDRI  AMI+AAE  
Sbjct: 12  GRIYDDFVATIGETPLVRLSRLGAEAGLAAELLAKLEMFNPLSSVKDRIALAMIEAAEAE 71

Query: 68  GTIEPGRTTLVEPTSGNTGIALAFVAAAKGYRLILTMPESMSVERRKMLKLLGAELVLTP 127
           G I PGR+TL+EPTSGNTGI LAF+AAA+GYRLILTMP +MS ERRK+    GA + LT 
Sbjct: 72  GRITPGRSTLIEPTSGNTGIGLAFIAAARGYRLILTMPANMSAERRKLFAFYGARVELTD 131

Query: 128 AAEGMKGAIRRADEIVATDPNAYMLQQFKNAANPEIHRNTTAEEIWKDTDGKADFLISGV 187
            A GM+GAI RA+ ++   P+++   QF N ANP  HR  TAEEIW+DT G  D LI+GV
Sbjct: 132 PAAGMRGAIDRAEALLEEIPDSFTPAQFSNPANPRAHRLRTAEEIWRDTGGSVDGLIAGV 191

Query: 188 GTGGTLTGVSEVLKARKPGFRTIAVEPEDSPVLSGGMPGPHKIQGIGAGFVPDVLKKDLI 247
           GTGGTLTG++ VLK R+PGFR  AVEP  SPVLSGG PGPH +QGIGAGF+PD L   L+
Sbjct: 192 GTGGTLTGIAGVLKERRPGFRAYAVEPAGSPVLSGGAPGPHGLQGIGAGFLPDTLDATLV 251

Query: 248 DEVVRISNQRAFETARKVAKLEGIPVGISSGAALAAALEIGSRPENEGKLIVVILPSFAE 307
           DE +++++  A   +R+VA+LEGIP GISSGAAL+AA+++ +RPE  G+ +VVIL S AE
Sbjct: 252 DETLQVTDDEALAMSRRVARLEGIPCGISSGAALSAAVQVAARPELAGQRLVVILASGAE 311

Query: 308 RYLSTALFEGLE 319
           RYLST LFEGL+
Sbjct: 312 RYLSTPLFEGLD 323


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: 349
Number of extensions: 16
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: 326
Length adjustment: 28
Effective length of query: 291
Effective length of database: 298
Effective search space:    86718
Effective search space used:    86718
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_041595022.1 HHAL_RS02830 (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.3195518.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-125  403.0   0.0   4.3e-125  402.8   0.0    1.0  1  NCBI__GCF_000015585.1:WP_041595022.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015585.1:WP_041595022.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.8   0.0  4.3e-125  4.3e-125       3     298 .]      20     319 ..      18     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 402.8 bits;  conditional E-value: 4.3e-125
                             TIGR01139   3 eliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgk.tiveatsGntGia 71 
                                            +iG+tPlvrL     +++ +ae+l+kle++nP ssvkdrialamie ae eg +++g+ t++e+tsGntGi+
  NCBI__GCF_000015585.1:WP_041595022.1  20 ATIGETPLVRLSrlgAEAGLAAELLAKLEMFNPLSSVKDRIALAMIEAAEAEGRITPGRsTLIEPTSGNTGIG 92 
                                           58*********9765678899*************************************889************ PP

                             TIGR01139  72 lamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpan 144
                                           la++aaargy+liltmp++ms errkl+  yGa++ Ltd+a gm+gai++ae l+ee p+++  + qf+npan
  NCBI__GCF_000015585.1:WP_041595022.1  93 LAFIAAARGYRLILTMPANMSAERRKLFAFYGARVELTDPAAGMRGAIDRAEALLEEIPDSF-TPAQFSNPAN 164
                                           ***********************************************************999.********** PP

                             TIGR01139 145 peihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGi 217
                                           p++hr  ta+ei++d+ g++d ++agvGtGGt+tG++ vlke +p ++++avePa spvlsgg pgph +qGi
  NCBI__GCF_000015585.1:WP_041595022.1 165 PRAHRLRTAEEIWRDTGGSVDGLIAGVGTGGTLTGIAGVLKERRPGFRAYAVEPAGSPVLSGGAPGPHGLQGI 237
                                           ************************************************************************* PP

                             TIGR01139 218 gagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtg 289
                                           gagf+P+ Ld +++de ++v+d+ea++++rr+a+ eGi  GissGaa+ aa++va ++e +++++vvil++ +
  NCBI__GCF_000015585.1:WP_041595022.1 238 GAGFLPDTLDATLVDETLQVTDDEALAMSRRVARLEGIPCGISSGAALSAAVQVAARPElAGQRLVVILASGA 310
                                           ************************************************************************* PP

                             TIGR01139 290 erYlstaLf 298
                                           erYlst+Lf
  NCBI__GCF_000015585.1:WP_041595022.1 311 ERYLSTPLF 319
                                           ********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (326 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: 13.45
//
[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