Alignments for a candidate for hisC in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Azospirillum brasilense Sp245

Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate AZOBR_RS20485 AZOBR_RS20485 histidinol-phosphate aminotransferase

Query= reanno::azobra:AZOBR_RS20485
         (364 letters)



>FitnessBrowser__azobra:AZOBR_RS20485
          Length = 364

 Score =  729 bits (1882), Expect = 0.0
 Identities = 364/364 (100%), Positives = 364/364 (100%)

Query: 1   MTQPNNGPAPRPGILDIAPYVGGEHAGHIRLASNEGALGPSPRAVEAYRAAAGELHRYPD 60
           MTQPNNGPAPRPGILDIAPYVGGEHAGHIRLASNEGALGPSPRAVEAYRAAAGELHRYPD
Sbjct: 1   MTQPNNGPAPRPGILDIAPYVGGEHAGHIRLASNEGALGPSPRAVEAYRAAAGELHRYPD 60

Query: 61  GGSAKLRKAIAERFGLDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAK 120
           GGSAKLRKAIAERFGLDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAK
Sbjct: 61  GGSAKLRKAIAERFGLDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAK 120

Query: 121 SVGATPVQAPETNLTTDVDSLLAHVTPRTRLVFVANPNNPTGTYITADEMARLHAGLPEN 180
           SVGATPVQAPETNLTTDVDSLLAHVTPRTRLVFVANPNNPTGTYITADEMARLHAGLPEN
Sbjct: 121 SVGATPVQAPETNLTTDVDSLLAHVTPRTRLVFVANPNNPTGTYITADEMARLHAGLPEN 180

Query: 181 AILVIDAAYAEYMNHNDYSAGQELVDRFPNVVMTRTFSKIFALGSVRLGWAYCPAGIADV 240
           AILVIDAAYAEYMNHNDYSAGQELVDRFPNVVMTRTFSKIFALGSVRLGWAYCPAGIADV
Sbjct: 181 AILVIDAAYAEYMNHNDYSAGQELVDRFPNVVMTRTFSKIFALGSVRLGWAYCPAGIADV 240

Query: 241 LNRVRGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREWFVQQVHGLGLKTHPSVTNF 300
           LNRVRGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREWFVQQVHGLGLKTHPSVTNF
Sbjct: 241 LNRVRGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREWFVQQVHGLGLKTHPSVTNF 300

Query: 301 VLVDFAGQTAGKDDAEAARLFLKGRGILVRQMPAYGLPSCLRVTIGTEAEMREVVQALKD 360
           VLVDFAGQTAGKDDAEAARLFLKGRGILVRQMPAYGLPSCLRVTIGTEAEMREVVQALKD
Sbjct: 301 VLVDFAGQTAGKDDAEAARLFLKGRGILVRQMPAYGLPSCLRVTIGTEAEMREVVQALKD 360

Query: 361 FLAA 364
           FLAA
Sbjct: 361 FLAA 364


Lambda     K      H
   0.319    0.136    0.405 

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: 622
Number of extensions: 15
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: 364
Length of database: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate AZOBR_RS20485 AZOBR_RS20485 (histidinol-phosphate aminotransferase)
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.26662.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.5e-96  309.3   0.0    1.7e-96  309.1   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS20485  AZOBR_RS20485 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS20485  AZOBR_RS20485 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.1   0.0   1.7e-96   1.7e-96       1     348 [.      11     360 ..      11     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 309.1 bits;  conditional E-value: 1.7e-96
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                               r+ i +++pY+ g     + + ++L+snE ++gps++++ea+++++ +lhrYpd  +++l++a+a+++g
  lcl|FitnessBrowser__azobra:AZOBR_RS20485  11 RPGILDIAPYVGG----EHAGHIRLASNEGALGPSPRAVEAYRAAAGELHRYPDGGSAKLRKAIAERFG 75 
                                               5678888999987....23378*********************************************** PP

                                 TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavle 138
                                               ++++ ++ g+Gsdeli llira++ pgd+vl++++ + mY++ ak  ga  +++p ++  + d++++l+
  lcl|FitnessBrowser__azobra:AZOBR_RS20485  76 LDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAKSVGATPVQAPETNL-TTDVDSLLA 143
                                               *******************************************************9988.69******* PP

                                 TIGR01141 139 aakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlv 203
                                                ++ +++lvf+a+PnnPtG++++++e+ ++ +   e+a+ V+D AY e+ ++       el+ ++pn+v
  lcl|FitnessBrowser__azobra:AZOBR_RS20485 144 HVTPRTRLVFVANPNNPTGTYITADEMARLHAGLpENAILVIDAAYAEYMNHndySAGQELVDRFPNVV 212
                                               **********************************89**************9977666789********* PP

                                 TIGR01141 204 vlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkerer 272
                                               ++rT+SK+f+L+++R+G a++ a i+++l++vr p+nvss a+ a+vaal+d +++e++  ++++ re+
  lcl|FitnessBrowser__azobra:AZOBR_RS20485 213 MTRTFSKIFALGSVRLGWAYCPAGIADVLNRVRGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREW 281
                                               ********************************************************************* PP

                                 TIGR01141 273 lleelkkleglevyeSkaNFvlikvke......daeelleallekgiivRdlksaeglleeclRitvGt 335
                                                 ++++ l gl++ +S +NFvl+++        dae++   l+ +gi+vR++ ++ gl + clR+t+Gt
  lcl|FitnessBrowser__azobra:AZOBR_RS20485 282 FVQQVHGL-GLKTHPSVTNFVLVDFAGqtagkdDAEAARLFLKGRGILVRQMPAY-GL-PSCLRVTIGT 347
                                               ********.8***************9899999777888888999*********99.85.********** PP

                                 TIGR01141 336 reenerllealke 348
                                               + e++++++alk+
  lcl|FitnessBrowser__azobra:AZOBR_RS20485 348 EAEMREVVQALKD 360
                                               **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (364 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: 7.05
//
[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