Alignments for a candidate for nagB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagB in Pedobacter sp. GW460-11-11-14-LB5

Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate CA265_RS21925 CA265_RS21925 glucosamine-6-phosphate deaminase

Query= reanno::Pedo557:CA265_RS21925
         (641 letters)



>FitnessBrowser__Pedo557:CA265_RS21925
          Length = 641

 Score = 1306 bits (3381), Expect = 0.0
 Identities = 641/641 (100%), Positives = 641/641 (100%)

Query: 1   MARLNLLEETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIA 60
           MARLNLLEETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIA
Sbjct: 1   MARLNLLEETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIA 60

Query: 61  VYAELVRLHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIP 120
           VYAELVRLHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIP
Sbjct: 61  VYAELVRLHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIP 120

Query: 121 DGTLALEDIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDL 180
           DGTLALEDIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDL
Sbjct: 121 DGTLALEDIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDL 180

Query: 181 TRRDAARDFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPA 240
           TRRDAARDFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPA
Sbjct: 181 TRRDAARDFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPA 240

Query: 241 TFLQLSDHVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTE 300
           TFLQLSDHVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTE
Sbjct: 241 TFLQLSDHVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTE 300

Query: 301 DDYNNNGMAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVI 360
           DDYNNNGMAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVI
Sbjct: 301 DDYNNNGMAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVI 360

Query: 361 IFSPHPDDDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGM 420
           IFSPHPDDDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGM
Sbjct: 361 IFSPHPDDDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGM 420

Query: 421 DNTHLKDLYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQAL 480
           DNTHLKDLYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQAL
Sbjct: 421 DNTHLKDLYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQAL 480

Query: 481 PFYESGKVQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRL 540
           PFYESGKVQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRL
Sbjct: 481 PFYESGKVQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRL 540

Query: 541 RKTEAWAQDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGD 600
           RKTEAWAQDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGD
Sbjct: 541 RKTEAWAQDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGD 600

Query: 601 DSREFWQRAEDRNRDTAKAYDELGLAEYEAMEAFVRWKFED 641
           DSREFWQRAEDRNRDTAKAYDELGLAEYEAMEAFVRWKFED
Sbjct: 601 DSREFWQRAEDRNRDTAKAYDELGLAEYEAMEAFVRWKFED 641


Lambda     K      H
   0.319    0.136    0.412 

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: 1522
Number of extensions: 51
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: 641
Length of database: 641
Length adjustment: 38
Effective length of query: 603
Effective length of database: 603
Effective search space:   363609
Effective search space used:   363609
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: 54 (25.4 bits)

Align candidate CA265_RS21925 CA265_RS21925 (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.27626.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.4e-77  245.8   0.0    7.6e-77  244.1   0.0    1.7  2  lcl|FitnessBrowser__Pedo557:CA265_RS21925  CA265_RS21925 glucosamine-6-phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS21925  CA265_RS21925 glucosamine-6-phosphate deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.1   0.0   7.6e-77   7.6e-77      16     248 ..      30     262 ..      18     267 .. 0.95
   2 ?   -2.0   0.0     0.093     0.093     123     150 ..     368     395 ..     366     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 244.1 bits;  conditional E-value: 7.6e-77
                                  TIGR00502  16 aariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvglseehPe 83 
                                                 a+ iae i+  k+ ++ p vlGlatG tP+ +y +l++l+k + +sfk+v+tfnldey  + +   +
  lcl|FitnessBrowser__Pedo557:CA265_RS21925  30 VAHRIAELIKS-KQANNTPAVLGLATGVTPIAVYAELVRLHKEEGLSFKNVITFNLDEYYPMAPTAAQ 96 
                                                46778888888.888899************************************************** PP

                                  TIGR00502  84 syhsfmyenffqhidikpeninilnGn..addleaecrryeekikslGkidlfllGiGadGhiafneP 149
                                                sy +fm+en+f+hidi ++n++i++G    +d+ a c +ye+ki +lG++d+++lGiG+ Ghi+fneP
  lcl|FitnessBrowser__Pedo557:CA265_RS21925  97 SYVTFMNENLFNHIDIDKKNVHIPDGTlaLEDIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEP 164
                                                **************************732589************************************ PP

                                  TIGR00502 150 gsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklve 217
                                                gs  +s tr++tl + t+   +r f+g  + vP ka+t+Gi+ti++++e++l++  ++ka+ +kk+ve
  lcl|FitnessBrowser__Pedo557:CA265_RS21925 165 GSAPNSGTRLVTLDDLTRRDAARDFGG-KTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVE 231
                                                *************************95.689************************************* PP

                                  TIGR00502 218 gsvnedvtisalqlhkkvivvadeeaaqelk 248
                                                g ++ dv+++ lql ++v  + d  aa+el 
  lcl|FitnessBrowser__Pedo557:CA265_RS21925 232 GEISGDVPATFLQLSDHVEFILDAPAASELT 262
                                                ***************************9985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.093
                                  TIGR00502 123 ekikslGkidlfllGiGadGhiafnePg 150
                                                + + s+G++ l l   G+d h+a+   g
  lcl|FitnessBrowser__Pedo557:CA265_RS21925 368 DDVISMGGTFLRLVDQGHDVHVAYQTSG 395
                                                567899*****************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (641 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: 19.08
//
[ok]

This GapMind analysis is from Sep 17 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