Alignments for a candidate for nagB in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagB in Pseudomonas litoralis 2SM5

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_090274005.1 BLU11_RS12960 glucosamine-6-phosphate deaminase

Query= SwissProt::O31458
         (249 letters)



>NCBI__GCF_900105005.1:WP_090274005.1
          Length = 240

 Score =  231 bits (588), Expect = 1e-65
 Identities = 120/243 (49%), Positives = 162/243 (66%), Gaps = 3/243 (1%)

Query: 1   MKILIAEHYEELCKLSAAIIKEQIQAKKDAVLGLATGSTPVGLYKQLISDYQAGEIDFSK 60
           MKI+   +Y EL   +  II + + +     LGLATGSTP+G Y+ L+  YQAG+I F  
Sbjct: 1   MKIITVNNYNELSSTAGQIIADLVSSNPRCTLGLATGSTPLGTYQYLVKRYQAGDISFKD 60

Query: 61  VTTFNLDEYAGLSPSHPQSYNHFMHEHLFQHINMQPDHIHIPQGDNPQLEAACKVYEDLI 120
           V TFNLDEY GL  +HP+SY  FMH++LF H+N+Q  + HIP  +   L++ C  Y  L+
Sbjct: 61  VQTFNLDEYCGLPRTHPESYFRFMHDNLFSHVNIQMQNRHIPCAEGGDLQSQCDAYNALL 120

Query: 121 RQAGGIDVQILGIGANGHIGFNEPGSDFEDRTRVVKLSESTIQANARFFGGDPVLVPRLA 180
           RQA  +D+Q+LGIG+NGHIGF EPG+ F+  T + +L+E T Q N RFF      VP  A
Sbjct: 121 RQA-TVDLQLLGIGSNGHIGFCEPGTPFDQETFLTQLAEKTRQDNQRFFNSLEE-VPTTA 178

Query: 181 ISMGIKTIMEFSKHIVLLASGEEKADAIQKMAEGPVTTDVPASILQKHNHVTVIADYKAA 240
           I+MGIK IM+ +K I+L+ASG+ KA+ I +M  GPVT  VPAS LQ+H + T+I D +AA
Sbjct: 179 ITMGIKNIMQ-AKSILLIASGKGKAECISQMVNGPVTEAVPASALQQHPNATIIVDEEAA 237

Query: 241 QKL 243
             L
Sbjct: 238 SLL 240


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: 178
Number of extensions: 7
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: 249
Length of database: 240
Length adjustment: 24
Effective length of query: 225
Effective length of database: 216
Effective search space:    48600
Effective search space used:    48600
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: 46 (22.3 bits)

Align candidate WP_090274005.1 BLU11_RS12960 (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.840638.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.5e-87  278.5   0.0    2.8e-87  278.3   0.0    1.0  1  NCBI__GCF_900105005.1:WP_090274005.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090274005.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.3   0.0   2.8e-87   2.8e-87       1     246 [.       1     239 [.       1     240 [] 0.98

  Alignments for each domain:
  == domain 1  score: 278.3 bits;  conditional E-value: 2.8e-87
                             TIGR00502   1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnlde 73 
                                           mk++++++y+els  a +iia+ +   +p       lGlatG+tP+g+y+ l++ y+ag++sfk+v tfnlde
  NCBI__GCF_900105005.1:WP_090274005.1   1 MKIITVNNYNELSSTAGQIIADLVSS-NPR----CTLGLATGSTPLGTYQYLVKRYQAGDISFKDVQTFNLDE 68 
                                           9***********************99.777....46************************************* PP

                             TIGR00502  74 yvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiaf 146
                                           y gl++ hPesy+ fm++n+f+h++i+ +n +i+  +  dl+++c  y+ +++++  +dl+llGiG++Ghi+f
  NCBI__GCF_900105005.1:WP_090274005.1  69 YCGLPRTHPESYFRFMHDNLFSHVNIQMQNRHIPCAEGGDLQSQCDAYNALLRQA-TVDLQLLGIGSNGHIGF 140
                                           ****************************************************997.79*************** PP

                             TIGR00502 147 nePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegs 219
                                            ePg+ +++ t + +l+e+t++ n rff+ ++++vP +a+t+Gik i+++k +ll++sGk kae + ++v+g+
  NCBI__GCF_900105005.1:WP_090274005.1 141 CEPGTPFDQETFLTQLAEKTRQDNQRFFN-SLEEVPTTAITMGIKNIMQAKSILLIASGKGKAECISQMVNGP 212
                                           ****************************9.9****************************************** PP

                             TIGR00502 220 vnedvtisalqlhkkvivvadeeaaqe 246
                                           v+e v++salq h ++++++deeaa+ 
  NCBI__GCF_900105005.1:WP_090274005.1 213 VTEAVPASALQQHPNATIIVDEEAASL 239
                                           ************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (240 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: 00:00:00.00
# Mc/sec: 14.81
//
[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 2024 update 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