Alignments for a candidate for hisC in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Shewanella amazonensis SB2B

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate 6937802 Sama_1943 histidinol-phosphate aminotransferase (RefSeq)

Query= SwissProt::P06986
         (356 letters)



>FitnessBrowser__SB2B:6937802
          Length = 362

 Score =  260 bits (665), Expect = 3e-74
 Identities = 158/350 (45%), Positives = 208/350 (59%), Gaps = 17/350 (4%)

Query: 9   LARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQ-QTLNRYPECQPKAVIENY 67
           LAR  + +L PYQSARR+GG+G++W+NANE P    F  T     NRYPECQP  +I  Y
Sbjct: 17  LARPELLSLEPYQSARRIGGSGEIWVNANESP----FNRTGIDGANRYPECQPPGLIAAY 72

Query: 68  AQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIGVECRTV 127
           A YAGV   +++  RGADE IELLIR FC PG+D+I    PTYGMY++SA T  V   T+
Sbjct: 73  AAYAGVAAHELVCGRGADEAIELLIRTFCVPGQDSIGIFSPTYGMYAISAATFNVAVNTL 132

Query: 128 PTLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAIVVADEAY 187
           P  +++ L    IS  L G K+V+VC+PNNPTG L+ P      +  T   A+VV DEAY
Sbjct: 133 PLAEDFSLP-DDIS-ALTGSKLVFVCNPNNPTGTLL-PLGEIARVAKTFPNALVVVDEAY 189

Query: 188 IEFC------PQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVIA 241
           IEF       P  S    +AE+ +L ILRTLSKAF LAG RCGF LA   V  L+M+VIA
Sbjct: 190 IEFAHNADGSPAQSATSLMAEFENLVILRTLSKAFGLAGARCGFLLAKPSVCELVMRVIA 249

Query: 242 PYPLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSETNYIL 301
           PYP+  PV+ IA +ALS  GI  MR  V  +  +   L  AL E      V  S  NY+L
Sbjct: 250 PYPVPVPVSVIAEKALSVMGIAQMRADVVLLNKQGARLALALTEAGL--SVLPSGGNYVL 307

Query: 302 ARFKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDAL 351
           A       + ++L   GI+ R +   P L   +RI+  + +++  +I+A+
Sbjct: 308 AFSNDVEVLARALTKAGIVAR-RYSHPRLKDAIRISYASEQQTDSIIEAI 356


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: 343
Number of extensions: 21
Number of successful extensions: 5
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: 362
Length adjustment: 29
Effective length of query: 327
Effective length of database: 333
Effective search space:   108891
Effective search space used:   108891
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 6937802 Sama_1943 (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.25017.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
      2e-93  299.0   0.0    2.2e-93  298.8   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937802  Sama_1943 histidinol-phosphate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937802  Sama_1943 histidinol-phosphate aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.8   0.0   2.2e-93   2.2e-93       1     348 [.      19     358 ..      19     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: 298.8 bits;  conditional E-value: 2.2e-93
                         TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeenill 77 
                                       r+++ +lepYq+ ar++g+++ ++ n+nE+Pf+ +          ++  +rYp++q+  l +a+a+y+gv + +++ 
  lcl|FitnessBrowser__SB2B:6937802  19 RPELLSLEPYQS-ARRIGGSGEIWVNANESPFNRT---------GIDGANRYPECQPPGLIAAYAAYAGVAAHELVC 85 
                                       678999******.9*******************99.........46678**************************** PP

                         TIGR01141  78 gnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasPn 153
                                       g+G+de+iellir+f+ pg d++ +++pty mY++sa++ ++ v + pl+ed+    ++++  a    klvf+++Pn
  lcl|FitnessBrowser__SB2B:6937802  86 GRGADEAIELLIRTFCVPGqDSIGIFSPTYGMYAISAATFNVAVNTLPLAEDF-SLPDDIS--ALTGSKLVFVCNPN 159
                                       *******************9********************************5.7888888..78999********* PP

                         TIGR01141 154 nPtGnllkreeiekvleevedalVVvDeAYieFsee......asvlellaeypnlvvlrTlSKafgLAglRvGyaia 224
                                       nPtG+ll   ei +v+++  +alVVvDeAYieF+++      +s+++l+ae++nlv+lrTlSKafgLAg R+G+++a
  lcl|FitnessBrowser__SB2B:6937802 160 NPTGTLLPLGEIARVAKTFPNALVVVDEAYIEFAHNadgspaQSATSLMAEFENLVILRTLSKAFGLAGARCGFLLA 236
                                       ******************999**************99999999********************************** PP

                         TIGR01141 225 naeiiealekvrapynvsslaleaavaalrdsd..kiektveevkkererlleelkkleglevyeSkaNFvlikvke 299
                                       ++++ e +++v+apy+v+++++ +a +al+     ++++ v  ++k+ +rl  +l++  gl+v +S +N+vl+  + 
  lcl|FitnessBrowser__SB2B:6937802 237 KPSVCELVMRVIAPYPVPVPVSVIAEKALSVMGiaQMRADVVLLNKQGARLALALTEA-GLSVLPSGGNYVLAFSN- 311
                                       *******************************998899999999**************9.8*************766. PP

                         TIGR01141 300 daeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                       d e l++al+++gi+ R  +  ++ l++++Ri+  ++++++ ++ea+ +
  lcl|FitnessBrowser__SB2B:6937802 312 DVEVLARALTKAGIVARRYS--HPRLKDAIRISYASEQQTDSIIEAIGR 358
                                       ******************99..5568*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (362 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.14
//
[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