Alignments for a candidate for hisC in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Acidovorax sp. GW101-3H11

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate Ac3H11_4729 Histidinol-phosphate aminotransferase (EC 2.6.1.9)

Query= uniprot:A0A2R7PAQ8
         (373 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4729
          Length = 374

 Score =  688 bits (1775), Expect = 0.0
 Identities = 347/374 (92%), Positives = 361/374 (96%), Gaps = 1/374 (0%)

Query: 1   MTTPA-SSPLQALARIRPDVRAMHSYVVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGS 59
           MT  A SSPLQALARIRPDVRAMH+Y VQPSTGMLKMDAMENPFRLPAHLQAALGQRLG+
Sbjct: 1   MTNAAPSSPLQALARIRPDVRAMHAYGVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGA 60

Query: 60  VALNRYPGDRIADLKAALAQYAGMPEGYGIVLGNGSDELITLLALACAQPGTGQRATMLA 119
           VALNRYPGDR+ DLKAALA+YAGMPEGYG+VLGNGSDELITLLALACAQPGTGQRATMLA
Sbjct: 61  VALNRYPGDRLLDLKAALAKYAGMPEGYGVVLGNGSDELITLLALACAQPGTGQRATMLA 120

Query: 120 PMPGFVMYPLSAQLQGLDFVGVPLTPDFELDEPAMLAAIGQHRPAITYIAYPNNPTATLW 179
           PMPGFVMYP+SAQLQGLDFV VPLT DFELDEPAMLAAI QH+PAITYIAYPNNPTATLW
Sbjct: 121 PMPGFVMYPMSAQLQGLDFVAVPLTADFELDEPAMLAAIAQHKPAITYIAYPNNPTATLW 180

Query: 180 DEGAVQRIIDAAGAQGGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAG 239
           DEGAVQRIIDAAGAQGGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAG
Sbjct: 181 DEGAVQRIIDAAGAQGGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAG 240

Query: 240 VRLGYLIGPSAFVSEIDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRVERATLIAA 299
           VRLGYLIGP+AFVSEIDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIR ER  ++AA
Sbjct: 241 VRLGYLIGPAAFVSEIDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRAERTQVLAA 300

Query: 300 LRQMPGVEKCWDSEANMVLIRVADSAKAYEGMKNRKVLVKNVSTMHPLLANCLRLTVGNA 359
           LRQMPGVEKCWDSEANM+LIRVADSA+AY+GMK RKVLVKNVSTMHPLLANCLRLTVG+A
Sbjct: 301 LRQMPGVEKCWDSEANMILIRVADSARAYDGMKTRKVLVKNVSTMHPLLANCLRLTVGDA 360

Query: 360 EDNAQMLAALQASL 373
            DNAQMLAALQASL
Sbjct: 361 SDNAQMLAALQASL 374


Lambda     K      H
   0.321    0.134    0.392 

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: 614
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: 373
Length of database: 374
Length adjustment: 30
Effective length of query: 343
Effective length of database: 344
Effective search space:   117992
Effective search space used:   117992
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 Ac3H11_4729 (Histidinol-phosphate aminotransferase (EC 2.6.1.9))
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.2163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    1.6e-87  279.6   0.0    1.9e-87  279.4   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4729  Histidinol-phosphate aminotransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4729  Histidinol-phosphate aminotransferase (EC 2.6.1.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.4   0.0   1.9e-87   1.9e-87       1     347 [.      17     371 ..      17     373 .. 0.94

  Alignments for each domain:
  == domain 1  score: 279.4 bits;  conditional E-value: 1.9e-87
                                        TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalel 60 
                                                      r++++++++Y      ++ ++++k++++EnPf  + ++++al ++l    l+rYp +  l+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4729  17 RPDVRAMHAYGV----QPSTGMLKMDAMENPFRLPAHLQAALGQRLGavALNRYPGDRLLDL 74 
                                                      689999999999....567789***********************99899************ PP

                                        TIGR01141  61 kealakylg.veeenillgnGsdelielliraflepg....davlvleptysmYevsakiag 117
                                                      k+alaky+g  e   ++lgnGsdeli+ll+ a+++pg    +++l+++p + mY++sa+++g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4729  75 KAALAKYAGmPEGYGVVLGNGSDELITLLALACAQPGtgqrATMLAPMPGFVMYPMSAQLQG 136
                                                      *********556789*********************8654347999**************** PP

                                        TIGR01141 118 aevkevplkedgqedleavle.aakekvklvflasPnnPtGnllkreeiekvleev.e.dal 176
                                                       + + vpl++d++ d +a+l+ +a++k+ ++++a+PnnPt +l ++  ++++++++ +  ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4729 137 LDFVAVPLTADFELDEPAMLAaIAQHKPAITYIAYPNNPTATLWDEGAVQRIIDAAgAqGGI 198
                                                      ***********999999999868899******************************9669** PP

                                        TIGR01141 177 VVvDeAYieFseeasvlellaeyp....nlvvlrTlSKafgLAglRvGyaianaeiiealek 234
                                                      VV+DeAY  F+++ ++++ ++  p    +++ +rTlSK+ gLAg+R+Gy+i+ a+ +++++k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4729 199 VVMDEAYQPFASR-TWIDRMRAEParnaHVLLMRTLSKF-GLAGVRLGYLIGPAAFVSEIDK 258
                                                      ************7.777776655444459*********5.6********************* PP

                                        TIGR01141 235 vrapynvsslaleaavaalrdsdkiektveevkkererlleelkklegle.vyeSkaNFvli 295
                                                      vr+pynvs+l +eaa+ al++++ ++++ +e+++er+++l++l++++g+e + +S+aN +li
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4729 259 VRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRAERTQVLAALRQMPGVEkCWDSEANMILI 320
                                                      **************************************************9*********** PP

                                        TIGR01141 296 kvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealk 347
                                                      +v  d++++++ ++ ++++v++++++++ll +clR+tvG +++n ++l+al+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4729 321 RVA-DSARAYDGMKTRKVLVKNVSTMHPLLANCLRLTVGDASDNAQMLAALQ 371
                                                      **9.*********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (374 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.07
//
[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