Alignments for a candidate for hisC in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Marinobacter adhaerens HP15

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate GFF2483 HP15_2427 histidinol-phosphate aminotransferase

Query= reanno::Marino:GFF2483
         (350 letters)



>FitnessBrowser__Marino:GFF2483
          Length = 350

 Score =  705 bits (1819), Expect = 0.0
 Identities = 350/350 (100%), Positives = 350/350 (100%)

Query: 1   MSKFWSPLVNDLVPYVPGEQPKMANLVKLNTNENPFGPSPKVIEAIQAELNDGLRLYPDP 60
           MSKFWSPLVNDLVPYVPGEQPKMANLVKLNTNENPFGPSPKVIEAIQAELNDGLRLYPDP
Sbjct: 1   MSKFWSPLVNDLVPYVPGEQPKMANLVKLNTNENPFGPSPKVIEAIQAELNDGLRLYPDP 60

Query: 61  EGESLRETIAAYHKITPEQIFLGNGSDEVLAHIFFGLFQHGEPILFPDITYSFYPVYCGL 120
           EGESLRETIAAYHKITPEQIFLGNGSDEVLAHIFFGLFQHGEPILFPDITYSFYPVYCGL
Sbjct: 61  EGESLRETIAAYHKITPEQIFLGNGSDEVLAHIFFGLFQHGEPILFPDITYSFYPVYCGL 120

Query: 121 YNIESKKVPLTESFEINPEDFKQPNGGVIFPNPNAPTGRYLELQYVEEILAANPNRVVVV 180
           YNIESKKVPLTESFEINPEDFKQPNGGVIFPNPNAPTGRYLELQYVEEILAANPNRVVVV
Sbjct: 121 YNIESKKVPLTESFEINPEDFKQPNGGVIFPNPNAPTGRYLELQYVEEILAANPNRVVVV 180

Query: 181 DEAYIDFGGESAITLVDKYPNLLVSQTLSKARSLAGLRVGFAVGHPDLIEALNRVKNSFN 240
           DEAYIDFGGESAITLVDKYPNLLVSQTLSKARSLAGLRVGFAVGHPDLIEALNRVKNSFN
Sbjct: 181 DEAYIDFGGESAITLVDKYPNLLVSQTLSKARSLAGLRVGFAVGHPDLIEALNRVKNSFN 240

Query: 241 SYPLDRLALAGAKAAYEDEAWFRKCCDGVISERERVTAVLEGLGFEVLPSKANFIFARHK 300
           SYPLDRLALAGAKAAYEDEAWFRKCCDGVISERERVTAVLEGLGFEVLPSKANFIFARHK
Sbjct: 241 SYPLDRLALAGAKAAYEDEAWFRKCCDGVISERERVTAVLEGLGFEVLPSKANFIFARHK 300

Query: 301 EQPGEVLAKGLREQGIIVRHFNKPRISEFLRITIGTVEQNDALIARLESL 350
           EQPGEVLAKGLREQGIIVRHFNKPRISEFLRITIGTVEQNDALIARLESL
Sbjct: 301 EQPGEVLAKGLREQGIIVRHFNKPRISEFLRITIGTVEQNDALIARLESL 350


Lambda     K      H
   0.319    0.139    0.410 

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: 674
Number of extensions: 17
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: 350
Length of database: 350
Length adjustment: 29
Effective length of query: 321
Effective length of database: 321
Effective search space:   103041
Effective search space used:   103041
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate GFF2483 HP15_2427 (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.3314.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    6.6e-99  317.0   0.0    7.4e-99  316.9   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2483  HP15_2427 histidinol-phosphate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2483  HP15_2427 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.9   0.0   7.4e-99   7.4e-99       4     348 ..       9     349 ..       6     350 .] 0.94

  Alignments for each domain:
  == domain 1  score: 316.9 bits;  conditional E-value: 7.4e-99
                           TIGR01141   4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylgveeenill 77 
                                         +++l pY+pg++ +   + vkLn+nEnPfgps+kv+ea+++el+  l++Ypdp++  l+e++a+y ++++e+i+l
  lcl|FitnessBrowser__Marino:GFF2483   9 VNDLVPYVPGEQPKMA-NLVKLNTNENPFGPSPKVIEAIQAELNdGLRLYPDPEGESLRETIAAYHKITPEQIFL 82 
                                         899******9777777.6*************************989***************************** PP

                           TIGR01141  78 gnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasP 152
                                         gnGsde++  ++  + + g+ +l+++ tys Y+v+  ++++e k+vpl+e+++ + e+++   + +  ++f  +P
  lcl|FitnessBrowser__Marino:GFF2483  83 GNGSDEVLAHIFFGLFQHGEPILFPDITYSFYPVYCGLYNIESKKVPLTESFEINPEDFK---QPNGGVIF-PNP 153
                                         ***************************************************999999998...55556666.89* PP

                           TIGR01141 153 nnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaianae 227
                                         n+PtG +l+ + +e++l++  + +VVvDeAYi+F +e s++ l+ +ypnl+v++TlSKa +LAglRvG+a+++++
  lcl|FitnessBrowser__Marino:GFF2483 154 NAPTGRYLELQYVEEILAANPNRVVVVDEAYIDFGGE-SAITLVDKYPNLLVSQTLSKARSLAGLRVGFAVGHPD 227
                                         *******************779**************7.************************************* PP

                           TIGR01141 228 iiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvke 299
                                         +ieal++v++++n   +++lal+ a+aa++d++ ++k+ + v++erer+++ l+ l g+ev +SkaNF++++ ke
  lcl|FitnessBrowser__Marino:GFF2483 228 LIEALNRVKNSFNsypLDRLALAGAKAAYEDEAWFRKCCDGVISERERVTAVLEGL-GFEVLPSKANFIFARHKE 301
                                         *********87543339***************************************.8***************99 PP

                           TIGR01141 300 .daeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                          + e l++ l e+giivR++++    ++e+lRit+Gt e+n++l++ l++
  lcl|FitnessBrowser__Marino:GFF2483 302 qPGEVLAKGLREQGIIVRHFNKP--RISEFLRITIGTVEQNDALIARLES 349
                                         778888899***********955..68******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (350 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: 6.13
//
[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