Alignments for a candidate for hisC in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Desulfovibrio vulgaris Miyazaki F

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate 8500145 DvMF_0908 histidinol-phosphate aminotransferase (RefSeq)

Query= reanno::Miya:8500145
         (387 letters)



>FitnessBrowser__Miya:8500145
          Length = 387

 Score =  770 bits (1987), Expect = 0.0
 Identities = 387/387 (100%), Positives = 387/387 (100%)

Query: 1   MCADKTASAGAPTGLPLASPSAVRPEVCGFKPYTPGLSIDEIRDRYGLAHVIKLASNENP 60
           MCADKTASAGAPTGLPLASPSAVRPEVCGFKPYTPGLSIDEIRDRYGLAHVIKLASNENP
Sbjct: 1   MCADKTASAGAPTGLPLASPSAVRPEVCGFKPYTPGLSIDEIRDRYGLAHVIKLASNENP 60

Query: 61  LGTSPVVQHALRHKADLAFRYAQSGNPRLTAAIAAHHGVPAERVVAGNGSDEIIDLIVRV 120
           LGTSPVVQHALRHKADLAFRYAQSGNPRLTAAIAAHHGVPAERVVAGNGSDEIIDLIVRV
Sbjct: 61  LGTSPVVQHALRHKADLAFRYAQSGNPRLTAAIAAHHGVPAERVVAGNGSDEIIDLIVRV 120

Query: 121 RAVPGVHNVVAFNPCFSIYELQTRLAGVEFRQAPLAADFSFDWDGLMALVDDATAVVFVT 180
           RAVPGVHNVVAFNPCFSIYELQTRLAGVEFRQAPLAADFSFDWDGLMALVDDATAVVFVT
Sbjct: 121 RAVPGVHNVVAFNPCFSIYELQTRLAGVEFRQAPLAADFSFDWDGLMALVDDATAVVFVT 180

Query: 181 TPDNPSGFCPPVADLERLAHALPAGCLLVVDEAYMDFCGDESAHSLLARVDEFPNLAVLR 240
           TPDNPSGFCPPVADLERLAHALPAGCLLVVDEAYMDFCGDESAHSLLARVDEFPNLAVLR
Sbjct: 181 TPDNPSGFCPPVADLERLAHALPAGCLLVVDEAYMDFCGDESAHSLLARVDEFPNLAVLR 240

Query: 241 TFSKSFGLAGLRLGYGILPVQLADYLRRVRLPFSVNILAEEAGLAALADDVFRTETLRVI 300
           TFSKSFGLAGLRLGYGILPVQLADYLRRVRLPFSVNILAEEAGLAALADDVFRTETLRVI
Sbjct: 241 TFSKSFGLAGLRLGYGILPVQLADYLRRVRLPFSVNILAEEAGLAALADDVFRTETLRVI 300

Query: 301 SEGRAALTEGLTALGCHVYPSKANFVMFRPAPTCKSAAHLFEELLRRGIIIRPLKSYGLP 360
           SEGRAALTEGLTALGCHVYPSKANFVMFRPAPTCKSAAHLFEELLRRGIIIRPLKSYGLP
Sbjct: 301 SEGRAALTEGLTALGCHVYPSKANFVMFRPAPTCKSAAHLFEELLRRGIIIRPLKSYGLP 360

Query: 361 DLLRVSVGSPDENAAFLKAAGEIMAHA 387
           DLLRVSVGSPDENAAFLKAAGEIMAHA
Sbjct: 361 DLLRVSVGSPDENAAFLKAAGEIMAHA 387


Lambda     K      H
   0.322    0.138    0.413 

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: 714
Number of extensions: 6
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate 8500145 DvMF_0908 (histidinol-phosphate aminotransferase (RefSeq))
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.8094.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.4e-98  315.2   0.0    2.7e-98  315.0   0.0    1.0  1  lcl|FitnessBrowser__Miya:8500145  DvMF_0908 histidinol-phosphate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8500145  DvMF_0908 histidinol-phosphate aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.0   0.0   2.7e-98   2.7e-98       1     349 []      24     383 ..      24     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: 315.0 bits;  conditional E-value: 2.7e-98
                         TIGR01141   1 rekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgve 71 
                                       r+++  ++pY+pg       +++g  +v+kL+snEnP+g+s+ v++al+++++   rY ++ + +l++a+a++ gv 
  lcl|FitnessBrowser__Miya:8500145  24 RPEVCGFKPYTPGlsideiRDRYGLAHVIKLASNENPLGTSPVVQHALRHKADLAFRYAQSGNPRLTAAIAAHHGVP 100
                                       6788899**********999999999*************************************************** PP

                         TIGR01141  72 eenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklv 147
                                       +e +++gnGsde+i+l++r  + pg ++v++++p +s+Ye+ +++ag+e +++pl++d++ d + + + +++ + +v
  lcl|FitnessBrowser__Miya:8500145 101 AERVVAGNGSDEIIDLIVRVRAVPGvHNVVAFNPCFSIYELQTRLAGVEFRQAPLAADFSFDWDGLMALVDDATAVV 177
                                       ***********************************************************9***************** PP

                         TIGR01141 148 flasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgLAglRvG 220
                                       f+++P+nP+G +   +++e+++++  + +l VvDeAY++F+++    s l  + e+pnl+vlrT+SK+fgLAglR+G
  lcl|FitnessBrowser__Miya:8500145 178 FVTTPDNPSGFCPPVADLERLAHALpAGCLLVVDEAYMDFCGDesaHSLLARVDEFPNLAVLRTFSKSFGLAGLRLG 254
                                       *************************88****************6666666777899********************* PP

                         TIGR01141 221 yaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikv 297
                                       y+i   +++++l++vr p++v+ la ea++aal d+ +  +t++ + ++r+ l+e+l++l g +vy+SkaNFv+++ 
  lcl|FitnessBrowser__Miya:8500145 255 YGILPVQLADYLRRVRLPFSVNILAEEAGLAALADDVFRTETLRVISEGRAALTEGLTAL-GCHVYPSKANFVMFRP 330
                                       ************************************************************.8*************96 PP

                         TIGR01141 298 ke...daeelleallekgiivRdlksaeglleeclRitvGtreenerllealkei 349
                                             a++l+e+ll++gii+R lks+ gl ++ lR++vG+++en ++l+a  ei
  lcl|FitnessBrowser__Miya:8500145 331 APtckSAAHLFEELLRRGIIIRPLKSY-GL-PDLLRVSVGSPDENAAFLKAAGEI 383
                                       5568899********************.85.*******************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (387 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.24
//
[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