Alignments for a candidate for hisC in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Shewanella loihica PV-4

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate 5209746 Shew_2199 histidinol-phosphate aminotransferase (RefSeq)

Query= SwissProt::P06986
         (356 letters)



>FitnessBrowser__PV4:5209746
          Length = 360

 Score =  286 bits (732), Expect = 6e-82
 Identities = 159/351 (45%), Positives = 221/351 (62%), Gaps = 13/351 (3%)

Query: 9   LARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQQTLNRYPECQPKAVIENYA 68
           LAR  +  L PYQSARR+GG G +W+NANE P          +LNRYPECQP  +I  YA
Sbjct: 18  LARPELLTLEPYQSARRIGGEGQIWINANESPF---INSDLDSLNRYPECQPPELITRYA 74

Query: 69  QYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIGVECRTVP 128
           +YAGV  +QVL SRGADE IELLIR FC PG+D+I    PTYGMY++SA+T  V  + + 
Sbjct: 75  EYAGVSNQQVLTSRGADEAIELLIRTFCIPGRDSIACFGPTYGMYAISAKTFNVGVKALR 134

Query: 129 TLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAIVVADEAYI 188
             D +QL  Q +  ++   K+V++C+PNNPTG +I P     ++  +    +VV DEAYI
Sbjct: 135 LDDEYQLP-QELCSQVGDAKLVFICNPNNPTGTVIAPDAIEAVIR-SLPDTLVVVDEAYI 192

Query: 189 EFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVIAPYPLSTP 248
           EFCP  S+A  L +Y +L +LRTLSKAFALAG RCGF LA  EVI ++M+VIAPYP+  P
Sbjct: 193 EFCPDYSVASLLDKYDNLIVLRTLSKAFALAGARCGFMLATPEVIEMVMRVIAPYPVPLP 252

Query: 249 VADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSETNYILARFKASS 308
           VA +A  ALS  GI  M+ +VAQ+ A  + L  AL+E     +V  +  N++LA F  ++
Sbjct: 253 VAKLAIDALSKDGIARMQTQVAQLKANGQRLADALREAGA--RVLPAYGNFVLAYFDQAN 310

Query: 309 AV-----FKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAE 354
            +        L   G++ R   K P+L+  +R +  +  +++ +I  L+A+
Sbjct: 311 EIKVGEMQARLKQTGVVAR-AYKDPALADAIRFSFASDAQTETLIAILKAD 360


Lambda     K      H
   0.319    0.135    0.396 

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: 353
Number of extensions: 17
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: 356
Length of database: 360
Length adjustment: 29
Effective length of query: 327
Effective length of database: 331
Effective search space:   108237
Effective search space used:   108237
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 5209746 Shew_2199 (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.31667.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.1e-100  322.0   0.0   2.5e-100  321.7   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209746  Shew_2199 histidinol-phosphate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209746  Shew_2199 histidinol-phosphate aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.7   0.0  2.5e-100  2.5e-100       1     347 [.      20     358 ..      20     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: 321.7 bits;  conditional E-value: 2.5e-100
                        TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeenillg 78 
                                      r+++  lepYq+ ar++g+++ ++ n+nE+Pf +s          l++l+rYp++q+ el +++a+y+gv+++++l++
  lcl|FitnessBrowser__PV4:5209746  20 RPELLTLEPYQS-ARRIGGEGQIWINANESPFINS---------DLDSLNRYPECQPPELITRYAEYAGVSNQQVLTS 87 
                                      678899******.9******************999.........5789****************************** PP

                        TIGR01141  79 nGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasPnnP 155
                                      +G+de+iellir+f+ pg d+++ + pty mY++sak+ ++ vk  +l+++   +l++ l  +  ++klvf+++PnnP
  lcl|FitnessBrowser__PV4:5209746  88 RGADEAIELLIRTFCIPGrDSIACFGPTYGMYAISAKTFNVGVKALRLDDEY--QLPQELCSQVGDAKLVFICNPNNP 163
                                      **************************************************95..444444479999************ PP

                        TIGR01141 156 tGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiieale 233
                                      tG+++  + ie+v+ +  d+lVVvDeAYieF++++sv++ll +y+nl+vlrTlSKaf+LAg R+G+++a++e+ie+++
  lcl|FitnessBrowser__PV4:5209746 164 TGTVIAPDAIEAVIRSLPDTLVVVDEAYIEFCPDYSVASLLDKYDNLIVLRTLSKAFALAGARCGFMLATPEVIEMVM 241
                                      ****************99************************************************************ PP

                        TIGR01141 234 kvrapynvsslaleaavaalrdsd..kiektveevkkererlleelkkleglevyeSkaNFvlikvke....daeell 305
                                      +v+apy+v+ +++++a+ al+++    ++ +v+++k++ +rl ++l++  g +v + ++NFvl+ +++    +  e+ 
  lcl|FitnessBrowser__PV4:5209746 242 RVIAPYPVPLPVAKLAIDALSKDGiaRMQTQVAQLKANGQRLADALREA-GARVLPAYGNFVLAYFDQaneiKVGEMQ 318
                                      ***********************9999**********************.8****************98888888999 PP

                        TIGR01141 306 eallekgiivRdlksaeglleeclRitvGtreenerllealk 347
                                       +l++ g++ R  k   + l +++R +  ++ ++e l+++lk
  lcl|FitnessBrowser__PV4:5209746 319 ARLKQTGVVARAYKD--PALADAIRFSFASDAQTETLIAILK 358
                                      *************94..457******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (360 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.64
//
[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