Alignments for a candidate for hisC in Algiphilus aromaticivorans DG1253

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Algiphilus aromaticivorans DG1253

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_052367594.1 U743_RS06100 histidinol-phosphate transaminase

Query= reanno::DvH:206463
         (373 letters)



>NCBI__GCF_000733765.1:WP_052367594.1
          Length = 380

 Score =  253 bits (646), Expect = 6e-72
 Identities = 148/355 (41%), Positives = 202/355 (56%), Gaps = 7/355 (1%)

Query: 21  PYVPGLSIDEIRDRFGLADVVKLASNENPLGTSPVVQRTLKTKADLAFRYAQSGNPRLTR 80
           PY PG+ IDE++ R GL+DV+KLASNENPLG SP     L+ +  LA RY   G   L  
Sbjct: 19  PYQPGMPIDELQRRLGLSDVIKLASNENPLGCSPQAAAVLRGEHQLA-RYPDGGGFALKA 77

Query: 81  AIAAHHGVAPERVVAGNGSDEIIDLLIRVRATPGKHNIVAFRPCFSIYELQAKFCG---- 136
            IAA HGVAPE+V  GNGS+++++ + R+   PG+  + + R  F++Y L A        
Sbjct: 78  KIAAFHGVAPEQVTLGNGSNDLLEFVARIFLGPGRAAMYS-RHAFAVYPLAAAAQNAPSV 136

Query: 137 -LEFRQADLRPDFTFDWDAFLAATDENTAIAFVTTPDNPSGWCPPVSELEHVARTLPPSC 195
            +  R  D    +  D   F  A  +  A  F+  P+NP+G C P   +      +P S 
Sbjct: 137 VVPARPVDAEDAYGHDLVGFARALSDEVAAIFIANPNNPTGTCLPGGAVADFLGEVPEST 196

Query: 196 LFVIDEAYMDFCGDEAAHSLLSRLDAFPNIAVLRTFSKSFGLAGLRLGYGILPERLADYL 255
           + V+DEAY D+        + + L   PN+ V RTFSK +GLA LRLGYG+    LAD L
Sbjct: 197 IVVLDEAYWDYQDPSTRPDIDALLARHPNLLVTRTFSKIYGLAALRLGYGLSHPALADLL 256

Query: 256 HRVRLPFSVNILAEEAGLAALEDTVFRSETLRVTAEGRAYIAEGLTALGCEVMPSWANFI 315
           +RVR PF+ N LA  AG AAL D  F +E++ + A  RA +   L+A G +V+PS ANF+
Sbjct: 257 NRVRQPFNNNSLALAAGEAALADQAFVAESVALNARERARLERELSARGLQVLPSHANFV 316

Query: 316 MFRPPTDATDLFEALLRRGIIIRPLKSYGLPQHLRVSVGNADENRRFIEACKEIL 370
                 DA  + + LL  GII+RP+ SY +P  LRVSVG   EN RF+ A   I+
Sbjct: 317 AVGFGRDAAPIHQGLLEAGIIVRPMGSYEMPHFLRVSVGTETENDRFLAALDGIM 371


Lambda     K      H
   0.323    0.139    0.422 

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: 391
Number of extensions: 25
Number of successful extensions: 4
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: 380
Length adjustment: 30
Effective length of query: 343
Effective length of database: 350
Effective search space:   120050
Effective search space used:   120050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate WP_052367594.1 U743_RS06100 (histidinol-phosphate transaminase)
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.3598485.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-105  338.1   0.0   2.9e-105  337.9   0.0    1.0  1  NCBI__GCF_000733765.1:WP_052367594.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000733765.1:WP_052367594.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.9   0.0  2.9e-105  2.9e-105       3     347 ..      13     368 ..      11     370 .. 0.96

  Alignments for each domain:
  == domain 1  score: 337.9 bits;  conditional E-value: 2.9e-105
                             TIGR01141   3 kikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                            i+ ++pYqpg      +r+lg ++v+kL+snEnP+g+s+++ + l+ e ++l rYpd  +++lk+++a++ g
  NCBI__GCF_000733765.1:WP_052367594.1  13 GIRGMAPYQPGmpidelQRRLGLSDVIKLASNENPLGCSPQAAAVLRGE-HQLARYPDGGGFALKAKIAAFHG 84 
                                           6999****************************************99999.*********************** PP

                             TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked.....gqedleavl 137
                                           v +e+++lgnGs++l+e+++r fl pg+a++++ +++++Y++ a++++a  + vp++         +dl  ++
  NCBI__GCF_000733765.1:WP_052367594.1  85 VAPEQVTLGNGSNDLLEFVARIFLGPGRAAMYSRHAFAVYPLAAAAQNAPSVVVPARPVdaedaYGHDLVGFA 157
                                           **************************************************99998876545556678999999 PP

                             TIGR01141 138 eaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlr 206
                                            a +++v  +f+a+PnnPtG++l    + ++l ev e+++VV+DeAY ++ +    ++   lla++pnl+v+r
  NCBI__GCF_000733765.1:WP_052367594.1 158 RALSDEVAAIFIANPNNPTGTCLPGGAVADFLGEVpESTIVVLDEAYWDYQDPstrPDIDALLARHPNLLVTR 230
                                           9**********************************99*************997677888889*********** PP

                             TIGR01141 207 TlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkk 279
                                           T+SK++gLA+lR+Gy+++++++++ l++vr+p+n +slal+a+ aal d+++++++v+ +++er+rl+ el++
  NCBI__GCF_000733765.1:WP_052367594.1 231 TFSKIYGLAALRLGYGLSHPALADLLNRVRQPFNNNSLALAAGEAALADQAFVAESVALNARERARLERELSA 303
                                           ************************************************************************9 PP

                             TIGR01141 280 leglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealk 347
                                             gl+v +S+aNFv + + +da+ + + lle+giivR ++s+e  ++++lR++vGt+ en+r+l+al+
  NCBI__GCF_000733765.1:WP_052367594.1 304 R-GLQVLPSHANFVAVGFGRDAAPIHQGLLEAGIIVRPMGSYE--MPHFLRVSVGTETENDRFLAALD 368
                                           9.8***************************************5..5*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (380 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: 00:00:00.00
# Mc/sec: 13.56
//
[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