Alignments for a candidate for cysK in Methylocystis bryophila S285

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Methylocystis bryophila S285

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_085770473.1 B1812_RS04170 cysteine synthase A

Query= BRENDA::C4ITG6
         (334 letters)



>NCBI__GCF_002117405.1:WP_085770473.1
          Length = 326

 Score =  459 bits (1181), Expect = e-134
 Identities = 228/313 (72%), Positives = 263/313 (84%), Gaps = 2/313 (0%)

Query: 23  GRGRIYDSILDTIGNTPLVRIDKFARENGVKANLLVKLEFFNPLASVKDRIGLAMIEALE 82
           GRGRIYDSI  TIG+TP+VR+D+ A E GVKANLL KLEFFNP+ASVKDRIG+AMIE+LE
Sbjct: 14  GRGRIYDSITQTIGDTPIVRLDRIAAEKGVKANLLAKLEFFNPIASVKDRIGVAMIESLE 73

Query: 83  KQGKAVPGKTVFVEPTSGNTGIALAFAAAAKGYRLILTMPETMSMERRKLLRLLGAELVL 142
           K G+  PGKTV +EPTSGNTGIALAF AAA+GYRLIL MPE+MS+ERRK+L LLGAELVL
Sbjct: 74  KSGRIAPGKTVLIEPTSGNTGIALAFVAAARGYRLILVMPESMSIERRKMLALLGAELVL 133

Query: 143 TEGAKGMKGAIAEAEAIG--NPNAIIPQQFENPANPEIHRLTTAEEIWNDTNGEADILIS 200
           T  A GMKGA+A+A  +   NP ++IPQQFENPANPEIHRLTTAEEIWNDT G  D  +S
Sbjct: 134 TPAALGMKGAVAKALELAAENPGSVIPQQFENPANPEIHRLTTAEEIWNDTAGAIDYFVS 193

Query: 201 GIGTGGTITGVGQVIKARKPSFKVVAVEPKDSPVLSGGAPGPHKIQGLGAGFAPKTLDTG 260
           G+GTGGTITGVGQ +K RKP  ++VAVEP+DS VLSG  PGPHKIQG+GAGF P  LD G
Sbjct: 194 GVGTGGTITGVGQALKTRKPDLRIVAVEPEDSAVLSGRPPGPHKIQGIGAGFVPSILDRG 253

Query: 261 IYDEIVQISNEDAFTNARLVARLEGIPVGISSGAALAAAIEVGKRSENAGKNIVVVIPSF 320
           + DE+V I N+ AF  AR +ARLEG+P GISSGAA+AAA+E+  R E AGKNIV++IPSF
Sbjct: 254 VIDEVVTIGNQTAFETARRLARLEGVPGGISSGAAVAAALEIAGRPEAAGKNIVLIIPSF 313

Query: 321 AERYLSTALFEGL 333
           AERYLSTALFEGL
Sbjct: 314 AERYLSTALFEGL 326


Lambda     K      H
   0.314    0.134    0.373 

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: 384
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: 334
Length of database: 326
Length adjustment: 28
Effective length of query: 306
Effective length of database: 298
Effective search space:    91188
Effective search space used:    91188
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: 42 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_085770473.1 B1812_RS04170 (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.1903261.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.5e-137  442.2   0.5     5e-137  442.0   0.5    1.0  1  NCBI__GCF_002117405.1:WP_085770473.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002117405.1:WP_085770473.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.0   0.5    5e-137    5e-137       1     298 []      22     323 ..      22     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 442.0 bits;  conditional E-value: 5e-137
                             TIGR01139   1 iseliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgk.tiveatsGntG 69 
                                           i+++iG+tP+vrL+    ++++ka++l+kle++nP +svkdri++amie+ ek+g + +gk +++e+tsGntG
  NCBI__GCF_002117405.1:WP_085770473.1  22 ITQTIGDTPIVRLDriaAEKGVKANLLAKLEFFNPIASVKDRIGVAMIESLEKSGRIAPGKtVLIEPTSGNTG 94 
                                           5899**********754567889*************************************9789********* PP

                             TIGR01139  70 ialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenp 142
                                           iala+vaaargy+lil+mpe+ms+errk+l  +GaelvLt++a gmkga++ka el++e+p +  +++qfenp
  NCBI__GCF_002117405.1:WP_085770473.1  95 IALAFVAAARGYRLILVMPESMSIERRKMLALLGAELVLTPAALGMKGAVAKALELAAENPGSV-IPQQFENP 166
                                           *************************************************************666.******** PP

                             TIGR01139 143 anpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiq 215
                                           anpeihr tta+ei++d+ g++d fv+gvGtGGtitGvg++lk+ kpd+++vaveP++s+vlsg  pgphkiq
  NCBI__GCF_002117405.1:WP_085770473.1 167 ANPEIHRLTTAEEIWNDTAGAIDYFVSGVGTGGTITGVGQALKTRKPDLRIVAVEPEDSAVLSGRPPGPHKIQ 239
                                           ************************************************************************* PP

                             TIGR01139 216 GigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpd 287
                                           Gigagf+P++Ld+ videv+++ +++a+etarrla+ eG+  GissGaavaaal++a ++e ++k+iv i+p+
  NCBI__GCF_002117405.1:WP_085770473.1 240 GIGAGFVPSILDRGVIDEVVTIGNQTAFETARRLARLEGVPGGISSGAAVAAALEIAGRPEaAGKNIVLIIPS 312
                                           ************************************************************99*********** PP

                             TIGR01139 288 tgerYlstaLf 298
                                           ++erYlstaLf
  NCBI__GCF_002117405.1:WP_085770473.1 313 FAERYLSTALF 323
                                           **********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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.12
//
[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 2024 update 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 original 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