Alignments for a candidate for cysK in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Magnetospirillum magneticum AMB-1

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_011382646.1 AMB_RS01005 cysteine synthase A

Query= BRENDA::Q2PZM5
         (319 letters)



>NCBI__GCF_000009985.1:WP_011382646.1
          Length = 319

 Score =  476 bits (1225), Expect = e-139
 Identities = 234/311 (75%), Positives = 276/311 (88%), Gaps = 1/311 (0%)

Query: 6   FRGKIYDSILDTVGATPLVRVNRLAEDAGAKAQIVGKLEFFNPLASVKDRIGFAMIDAAE 65
           FRGKIYDSI+DT+GATPLVR  R+A +AG+KA IVGKLEFFNPLASVKDRIGFAMI+AAE
Sbjct: 8   FRGKIYDSIIDTIGATPLVRFKRMAAEAGSKADIVGKLEFFNPLASVKDRIGFAMIEAAE 67

Query: 66  RAGTIEPGRTTLVEPTSGNTGIALAFVAAAKGYRLILTMPESMSVERRKMLKLLGAELVL 125
            +G ++PG T ++EPTSGNTGIALAFVAAAKGY+LIL MPESMS+ERRKML+LLGAE+VL
Sbjct: 68  VSGQLKPGGT-IIEPTSGNTGIALAFVAAAKGYKLILCMPESMSLERRKMLQLLGAEIVL 126

Query: 126 TPAAEGMKGAIRRADEIVATDPNAYMLQQFKNAANPEIHRNTTAEEIWKDTDGKADFLIS 185
           TPA++GM GA+R+A+E++A+ P A M QQFKN ANP IH  TTAEEIW DT+GK D ++S
Sbjct: 127 TPASKGMTGAVRQAEELLASTPGAIMPQQFKNEANPAIHERTTAEEIWNDTNGKVDIIVS 186

Query: 186 GVGTGGTLTGVSEVLKARKPGFRTIAVEPEDSPVLSGGMPGPHKIQGIGAGFVPDVLKKD 245
           GVGTGGT++G+  VLKARKPG + +AVEPEDSPVLSGG PGPHKIQGIGAGFVPD+L K 
Sbjct: 187 GVGTGGTISGIGHVLKARKPGLKMVAVEPEDSPVLSGGAPGPHKIQGIGAGFVPDILDKG 246

Query: 246 LIDEVVRISNQRAFETARKVAKLEGIPVGISSGAALAAALEIGSRPENEGKLIVVILPSF 305
           +IDE+++I N+ A  TARK AKLEG+PVGISSGAA+AAALE+GSRPEN GKLIV I+PSF
Sbjct: 247 VIDEILQIGNETALATARKAAKLEGVPVGISSGAAIAAALELGSRPENAGKLIVAIIPSF 306

Query: 306 AERYLSTALFE 316
           AERYLSTALF+
Sbjct: 307 AERYLSTALFD 317


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: 413
Number of extensions: 13
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: 319
Length adjustment: 28
Effective length of query: 291
Effective length of database: 291
Effective search space:    84681
Effective search space used:    84681
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_011382646.1 AMB_RS01005 (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.27059.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-136  439.2   1.7   4.3e-136  439.0   1.7    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011382646.1  AMB_RS01005 cysteine synthase A


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011382646.1  AMB_RS01005 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.0   1.7  4.3e-136  4.3e-136       3     298 .]      18     316 ..      16     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 439.0 bits;  conditional E-value: 4.3e-136
                                 TIGR01139   3 eliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGnt 68 
                                               ++iG tPlvr +    +++ ka+++ kle++nP +svkdri++amie ae +g+lk+g ti+e+tsGnt
  lcl|NCBI__GCF_000009985.1:WP_011382646.1  18 DTIGATPLVRFKrmaAEAGSKADIVGKLEFFNPLASVKDRIGFAMIEAAEVSGQLKPGGTIIEPTSGNT 86 
                                               79*********97544567899*********************************************** PP

                                 TIGR01139  69 GialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllk 137
                                               Giala+vaaa+gyklil+mpe+mslerrk+l+ +Gae+vLt++++gm+ga+++aeel+++tp   ++++
  lcl|NCBI__GCF_000009985.1:WP_011382646.1  87 GIALAFVAAAKGYKLILCMPESMSLERRKMLQLLGAEIVLTPASKGMTGAVRQAEELLASTPG-AIMPQ 154
                                               **************************************************************5.55*** PP

                                 TIGR01139 138 qfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsg 206
                                               qf+n+anp+ih++tta+ei++d++gk+d++v+gvGtGGti+G+g+vlk  kp +k+vaveP++spvlsg
  lcl|NCBI__GCF_000009985.1:WP_011382646.1 155 QFKNEANPAIHERTTAEEIWNDTNGKVDIIVSGVGTGGTISGIGHVLKARKPGLKMVAVEPEDSPVLSG 223
                                               ********************************************************************* PP

                                 TIGR01139 207 gkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkl 275
                                               g pgphkiqGigagf+P++Ldk vide++++ +e+a++tar+ ak eG+ vGissGaa+aaal++  ++
  lcl|NCBI__GCF_000009985.1:WP_011382646.1 224 GAPGPHKIQGIGAGFVPDILDKGVIDEILQIGNETALATARKAAKLEGVPVGISSGAAIAAALELGSRP 292
                                               ********************************************************************9 PP

                                 TIGR01139 276 e.kdkkivvilpdtgerYlstaLf 298
                                               e ++k+iv+i+p+++erYlstaLf
  lcl|NCBI__GCF_000009985.1:WP_011382646.1 293 EnAGKLIVAIIPSFAERYLSTALF 316
                                               99*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (319 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: 8.44
//
[ok]

This GapMind analysis is from Apr 09 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