Alignments for a candidate for cysK in Methylobacterium sp. 4-46 Apr-46

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Methylobacterium sp. 4-46 Apr-46

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_012334196.1 M446_RS21395 cysteine synthase A

Query= BRENDA::C4ITG6
         (334 letters)



>NCBI__GCF_000019365.1:WP_012334196.1
          Length = 327

 Score =  427 bits (1099), Expect = e-124
 Identities = 213/320 (66%), Positives = 257/320 (80%), Gaps = 3/320 (0%)

Query: 16  SKDAEAAGRGRIYDSILDTIGNTPLVRIDKFARENGVKANLLVKLEFFNPLASVKDRIGL 75
           S    A G GR++ SI +TIGNTPLVR+++  RE GV+A +L+KLEFFNP+ASVKDRIG+
Sbjct: 9   SDTGRAPGHGRVFGSITETIGNTPLVRLNRLPRERGVEAEILLKLEFFNPIASVKDRIGV 68

Query: 76  AMIEALEKQGKAVPGKTVFVEPTSGNTGIALAFAAAAKGYRLILTMPETMSMERRKLLRL 135
            MI+ALE  G   PG T+ VEPTSGNTGIALAF AAA+GYRLIL MPETMS+ERRK+L  
Sbjct: 69  NMIDALEASGDLKPGGTL-VEPTSGNTGIALAFVAAARGYRLILVMPETMSLERRKMLAF 127

Query: 136 LGAELVLTEGAKGMKGAIAEAEAIGN--PNAIIPQQFENPANPEIHRLTTAEEIWNDTNG 193
           LGAELVLT G +GMKGA+A+AE +    P +++PQQF NPANPEIHR TTAEEIWNDT G
Sbjct: 128 LGAELVLTPGPQGMKGAVAKAEELLREIPGSVMPQQFNNPANPEIHRKTTAEEIWNDTQG 187

Query: 194 EADILISGIGTGGTITGVGQVIKARKPSFKVVAVEPKDSPVLSGGAPGPHKIQGLGAGFA 253
             D+ +SG+GTGGTITGVGQV+K R P  ++VAVEP+DSPVLSGG PGPHKIQG+GAGF 
Sbjct: 188 RLDVFVSGVGTGGTITGVGQVLKPRLPQLRLVAVEPEDSPVLSGGNPGPHKIQGIGAGFV 247

Query: 254 PKTLDTGIYDEIVQISNEDAFTNARLVARLEGIPVGISSGAALAAAIEVGKRSENAGKNI 313
           P  LD  + DE+V +SN+ AF  ARL+ RLEGIP GIS+GA +AAA+E+G R EN GK I
Sbjct: 248 PNVLDRDVIDEVVTVSNQTAFETARLLGRLEGIPGGISTGANVAAALEIGARPENRGKRI 307

Query: 314 VVVIPSFAERYLSTALFEGL 333
           V V  SFAERY+S+ALF+G+
Sbjct: 308 VTVACSFAERYISSALFDGI 327


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: 370
Number of extensions: 15
Number of successful extensions: 3
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: 327
Length adjustment: 28
Effective length of query: 306
Effective length of database: 299
Effective search space:    91494
Effective search space used:    91494
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_012334196.1 M446_RS21395 (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.1172199.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-138  445.7   0.0   4.5e-138  445.5   0.0    1.0  1  NCBI__GCF_000019365.1:WP_012334196.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019365.1:WP_012334196.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.5   0.0  4.5e-138  4.5e-138       1     298 []      24     324 ..      24     324 .. 0.98

  Alignments for each domain:
  == domain 1  score: 445.5 bits;  conditional E-value: 4.5e-138
                             TIGR01139   1 iseliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGi 70 
                                           i+e+iGntPlvrLn   ++ +++ae+l+kle++nP +svkdri+++mi   e +g lk+g t+ve+tsGntGi
  NCBI__GCF_000019365.1:WP_012334196.1  24 ITETIGNTPLVRLNrlpRERGVEAEILLKLEFFNPIASVKDRIGVNMIDALEASGDLKPGGTLVEPTSGNTGI 96 
                                           689***********876678999************************************************** PP

                             TIGR01139  71 alamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpa 143
                                           ala+vaaargy+lil+mpetmslerrk+l  +GaelvLt+g +gmkga++kaeel++e p +  +++qf+npa
  NCBI__GCF_000019365.1:WP_012334196.1  97 ALAFVAAARGYRLILVMPETMSLERRKMLAFLGAELVLTPGPQGMKGAVAKAEELLREIPGSV-MPQQFNNPA 168
                                           ************************************************************666.********* PP

                             TIGR01139 144 npeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqG 216
                                           npeihrktta+ei++d++g+ld+fv+gvGtGGtitGvg+vlk   p++++vaveP++spvlsgg+pgphkiqG
  NCBI__GCF_000019365.1:WP_012334196.1 169 NPEIHRKTTAEEIWNDTQGRLDVFVSGVGTGGTITGVGQVLKPRLPQLRLVAVEPEDSPVLSGGNPGPHKIQG 241
                                           ************************************************************************* PP

                             TIGR01139 217 igagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdt 288
                                           igagf+P+vLd++videv++vs+++a+etar l + eGi  Gis+Ga+vaaal++  ++e ++k+iv++++++
  NCBI__GCF_000019365.1:WP_012334196.1 242 IGAGFVPNVLDRDVIDEVVTVSNQTAFETARLLGRLEGIPGGISTGANVAAALEIGARPEnRGKRIVTVACSF 314
                                           *******************************************************999998************ PP

                             TIGR01139 289 gerYlstaLf 298
                                           +erY+s aLf
  NCBI__GCF_000019365.1:WP_012334196.1 315 AERYISSALF 324
                                           ********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (327 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: 13.07
//
[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