Alignments for a candidate for nagB in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagB in Halomonas desiderata SP1

Align Probable glucosamine-6-phosphate deaminase 2; GlcN6P deaminase 2; GNPDA 2; Glucosamine-6-phosphate isomerase 2; EC 3.5.99.6 (characterized)
to candidate WP_086511255.1 BZY95_RS17935 glucosamine-6-phosphate deaminase

Query= SwissProt::O31458
         (249 letters)



>NCBI__GCF_002151265.1:WP_086511255.1
          Length = 258

 Score =  241 bits (616), Expect = 8e-69
 Identities = 120/246 (48%), Positives = 169/246 (68%), Gaps = 2/246 (0%)

Query: 1   MKILIAEHYEELCKLSAAIIKEQIQAKKDAVLGLATGSTPVGLYKQLISDYQAGEIDFSK 60
           M ++I  + E + +L A II++Q+ AK D+VLGLATG+TP+ LY++L+  +QA  +   +
Sbjct: 1   MDLIIVHNVERMAQLGANIIQQQLSAKPDSVLGLATGATPLALYRELVVRHQATRLTLDQ 60

Query: 61  VTTFNLDEYAGLSPSHPQSYNHFMHEHLFQHINMQPDHIHIPQGDNPQLEAACKVYEDLI 120
           +TTFNLDEY GL P HP SY H+M  HLF  + + P   H+P G  P  +A  + YE  +
Sbjct: 61  LTTFNLDEYLGLGPDHPASYAHYMRRHLFGPLQLDPQRTHLPDGLAPDPQAEARRYEAQL 120

Query: 121 RQAGGIDVQILGIGANGHIGFNEPGSDFEDRTRVVKLSESTIQANARFFGGDPVLVPRLA 180
           + AGG+D+Q+LGIG NGHIGFNEPGS  + RTRVV+LS +T+ AN R F  D  + P  A
Sbjct: 121 QAAGGVDLQLLGIGLNGHIGFNEPGSPLDSRTRVVRLSATTLAANRRHFPADAEM-PTHA 179

Query: 181 ISMGIKTIMEFSKHIVLLASGEEKADAIQKMAEGPVTTDVPASILQKHNHVTVIADYKAA 240
           I++GI  I+E ++H++LLA+G  KA A+ +  EGPVT  +PAS+LQ+H +V+VI D  AA
Sbjct: 180 ITLGIGNILE-ARHLLLLATGRAKARAVAEALEGPVTATLPASVLQRHPNVSVILDAAAA 238

Query: 241 QKLKSA 246
             L  A
Sbjct: 239 AALSPA 244


Lambda     K      H
   0.317    0.134    0.382 

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: 196
Number of extensions: 7
Number of successful extensions: 2
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: 249
Length of database: 258
Length adjustment: 24
Effective length of query: 225
Effective length of database: 234
Effective search space:    52650
Effective search space used:    52650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_086511255.1 BZY95_RS17935 (glucosamine-6-phosphate deaminase)
to HMM TIGR00502 (nagB: glucosamine-6-phosphate deaminase (EC 3.5.99.6))

# 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.carbon/TIGR00502.hmm
# target sequence database:        /tmp/gapView.1048.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00502  [M=259]
Accession:   TIGR00502
Description: nagB: glucosamine-6-phosphate deaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.2e-85  272.1   0.0    2.6e-85  271.9   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511255.1  BZY95_RS17935 glucosamine-6-phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511255.1  BZY95_RS17935 glucosamine-6-phosphate deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.9   0.0   2.6e-85   2.6e-85       1     248 [.       1     242 [.       1     250 [. 0.98

  Alignments for each domain:
  == domain 1  score: 271.9 bits;  conditional E-value: 2.6e-85
                                 TIGR00502   1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtf 69 
                                               m l+i+++ e +++l a+ii++++ + kpd     vlGlatG+tP+ ly++l+  ++a ++ +++++tf
  lcl|NCBI__GCF_002151265.1:WP_086511255.1   1 MDLIIVHNVERMAQLGANIIQQQLSA-KPD-S---VLGLATGATPLALYRELVVRHQATRLTLDQLTTF 64 
                                               889***********************.999.5...9********************************* PP

                                 TIGR00502  70 nldeyvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGi 138
                                               nldey+gl ++hP sy ++m +++f  +++ p++ ++++G a+d +ae rrye +++ +G++dl+llGi
  lcl|NCBI__GCF_002151265.1:WP_086511255.1  65 NLDEYLGLGPDHPASYAHYMRRHLFGPLQLDPQRTHLPDGLAPDPQAEARRYEAQLQAAGGVDLQLLGI 133
                                               ********************************************************************* PP

                                 TIGR00502 139 GadGhiafnePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGke 207
                                               G +Ghi+fnePgs l+srtrv++l+  t+ an r+f++d  ++P +a+t+Gi+ il+++++lll++G+ 
  lcl|NCBI__GCF_002151265.1:WP_086511255.1 134 GLNGHIGFNEPGSPLDSRTRVVRLSATTLAANRRHFPADA-EMPTHAITLGIGNILEARHLLLLATGRA 201
                                               *************************************886.68************************** PP

                                 TIGR00502 208 kaeavkklvegsvnedvtisalqlhkkvivvadeeaaqelk 248
                                               ka+av +++eg+v+ ++++s+lq h +v v+ d +aa  l 
  lcl|NCBI__GCF_002151265.1:WP_086511255.1 202 KARAVAEALEGPVTATLPASVLQRHPNVSVILDAAAAAALS 242
                                               ***********************************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (258 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: 8.96
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources