Alignments for a candidate for glk in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Azospirillum brasilense Sp245

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate AZOBR_RS05405 AZOBR_RS05405 glucokinase

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__azobra:AZOBR_RS05405
          Length = 311

 Score =  259 bits (663), Expect = 5e-74
 Identities = 138/305 (45%), Positives = 184/305 (60%), Gaps = 4/305 (1%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLE--EHKVEVKDGCIAI 63
           LV D+G TNAR  L D     I  ++     D+PSLEA    YL    H      G  AI
Sbjct: 1   LVADIGATNARFGLIDGTG--IHGSRVLRCADFPSLEAAALAYLGGVAHDARPSRGAFAI 58

Query: 64  ACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAE 123
           A P+TGD V MTN  W+FS AE++  LG   L +INDFTAV++++P L    + Q G   
Sbjct: 59  AGPVTGDAVLMTNRGWSFSTAEVRGKLGLERLAVINDFTAVALSVPRLTAADVRQVGEGA 118

Query: 124 PVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGH 183
           PV G+ + V G G+GLGV+ LV   + W +L  EGGHV  AP S+ E+ +L  LR    H
Sbjct: 119 PVPGRVVGVVGPGSGLGVSGLVPGAEGWTALAAEGGHVTMAPVSDRESAVLAQLRKSFEH 178

Query: 184 VSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGR 243
           VSAERVLSGPGLVNLY+A+   D++ PE   P  +++ A A++   C  A+ +FC ++G 
Sbjct: 179 VSAERVLSGPGLVNLYQALCVLDHQEPEPFTPAQVSDAATANTNPHCVEAVEMFCAMLGT 238

Query: 244 FGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDN 303
             GNLAL LG  GG++IAGGIVP+    F  S FR  F +KGR ++++  IP Y+I H+ 
Sbjct: 239 VAGNLALTLGARGGIYIAGGIVPKLGTLFTHSRFRKRFMEKGRMRDFLAPIPTYVITHEL 298

Query: 304 PGLLG 308
           P  LG
Sbjct: 299 PAFLG 303


Lambda     K      H
   0.322    0.141    0.426 

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: 317
Number of extensions: 17
Number of successful extensions: 3
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: 321
Length of database: 311
Length adjustment: 27
Effective length of query: 294
Effective length of database: 284
Effective search space:    83496
Effective search space used:    83496
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate AZOBR_RS05405 AZOBR_RS05405 (glucokinase)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

# 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/TIGR00749.hmm
# target sequence database:        /tmp/gapView.4989.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00749  [M=315]
Accession:   TIGR00749
Description: glk: glucokinase
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-96  308.6   0.0    3.1e-96  308.3   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS05405  AZOBR_RS05405 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS05405  AZOBR_RS05405 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.3   0.0   3.1e-96   3.1e-96       1     313 [.       1     303 [.       1     305 [. 0.96

  Alignments for each domain:
  == domain 1  score: 308.3 bits;  conditional E-value: 3.1e-96
                                 TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdf 69 
                                               lv+diG tnar++l+      i+  +++++ dfpslea+   yl   +   + p +g+faia+P++gd 
  lcl|FitnessBrowser__azobra:AZOBR_RS05405   1 LVADIGATNARFGLI--DGTGIHGSRVLRCADFPSLEAAALAYLGGVAHDAR-PSRGAFAIAGPVTGDA 66 
                                               89************5..56679999********************9998865.89************** PP

                                 TIGR00749  70 vrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlG 138
                                               v +tn+ W++s +e++ +l+l++l +indf+ava++++ l   d+ q+g   ++++  + ++G+G GlG
  lcl|FitnessBrowser__azobra:AZOBR_RS05405  67 VLMTNRGWSFSTAEVRGKLGLERLAVINDFTAVALSVPRLTAADVRQVGEGAPVPGRVVGVVGPGSGLG 135
                                               ********************************************************************* PP

                                 TIGR00749 139 vatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkge 207
                                               v+ l++ + + + +la+eGghv +aP s+ e  +l  lrk +++vsaervlsG+Glv++y+al   +  
  lcl|FitnessBrowser__azobra:AZOBR_RS05405 136 VSGLVP-GAEGWTALAAEGGHVTMAPVSDRESAVLAQLRKSFEHVSAERVLSGPGLVNLYQALCVLD-- 201
                                               ******.8888****************************************************9988.. PP

                                 TIGR00749 208 revsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiel 276
                                                   +   e  ++ ++s+aa +++++ + +a+e+f+++lG++agnlal+lgarGG+y+aGGivP++  l
  lcl|FitnessBrowser__azobra:AZOBR_RS05405 202 ----HQEPEPFTPAQVSDAATANTNPHCVEAVEMFCAMLGTVAGNLALTLGARGGIYIAGGIVPKLGTL 266
                                               ....23347899********************************************************* PP

                                 TIGR00749 277 lkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313
                                               + +s fr++f +kGr++++la iP +v+ ++ + +lG
  lcl|FitnessBrowser__azobra:AZOBR_RS05405 267 FTHSRFRKRFMEKGRMRDFLAPIPTYVITHELPAFLG 303
                                               *******************************999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (311 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: 11.74
//
[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