GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Moritella dasanensis ArB 0140

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_017222136.1 A923_RS0113155 glucokinase

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



>NCBI__GCF_000276805.1:WP_017222136.1
          Length = 319

 Score =  325 bits (832), Expect = 1e-93
 Identities = 158/316 (50%), Positives = 215/316 (68%)

Query: 5   ALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIA 64
           ++V DVGGTN RLA+CD+ +G +S+ K ++  ++ +LEA +  Y      E+   C+ IA
Sbjct: 3   SVVADVGGTNIRLAVCDLETGALSELKEFACAEFVTLEAALAQYFAALSGEITHLCVGIA 62

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
           CP+  D V MTN  W FS   ++  L  + L IIND+TA+S+A+P L  E  IQ G  E 
Sbjct: 63  CPVENDHVVMTNLNWEFSKQALQDKLKLASLHIINDYTAISLAVPFLSAEEKIQIGAGEC 122

Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184
                 AV+G GTGLGV+H+V    +W+SL GEGGHV F PN+ E+A IL +L+ + GHV
Sbjct: 123 QTDGVTAVFGPGTGLGVSHIVKAAGKWISLDGEGGHVSFTPNTPEQADILCLLQTQFGHV 182

Query: 185 SAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRF 244
           SAER+LSG GLVNLY+ +     +  +  +PKD+T+ AL  SC   R++L++FC +MG F
Sbjct: 183 SAERILSGQGLVNLYKCLCTLSEQEAKFDQPKDVTKAALDGSCDIARKSLAVFCQVMGGF 242

Query: 245 GGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNP 304
            GNLALNL   GG++IAGGIVPRF++FF+AS FR  FE+KGRFK+Y+  IP +LI HDNP
Sbjct: 243 AGNLALNLACTGGIYIAGGIVPRFVDFFQASEFRRCFEEKGRFKDYLTAIPTFLITHDNP 302

Query: 305 GLLGSGAHLRQTLGHI 320
           GLLG+  +LRQ L  I
Sbjct: 303 GLLGASVYLRQELTSI 318


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: 337
Number of extensions: 14
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: 321
Length of database: 319
Length adjustment: 28
Effective length of query: 293
Effective length of database: 291
Effective search space:    85263
Effective search space used:    85263
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 WP_017222136.1 A923_RS0113155 (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.1847603.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.4e-106  339.6   0.2   1.1e-105  339.4   0.2    1.0  1  NCBI__GCF_000276805.1:WP_017222136.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017222136.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.4   0.2  1.1e-105  1.1e-105       2     314 ..       5     307 ..       4     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 339.4 bits;  conditional E-value: 1.1e-105
                             TIGR00749   2 vgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrltn 74 
                                           v+d+GGtn rla+++  +g ++ +k + + +f  lea++ +y      e+ +    c+ ia+P+ +d v +tn
  NCBI__GCF_000276805.1:WP_017222136.1   5 VADVGGTNIRLAVCDLETGALSELKEFACAEFVTLEAALAQYFAALSGEITH---LCVGIACPVENDHVVMTN 74 
                                           89*****************************************999999988...9***************** PP

                             TIGR00749  75 ldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsd 147
                                           l+W++s + l+ +l la l++ind++a+++a++ l  e+ iq+g+ ++++++  a++G+GtGlGv+++++ + 
  NCBI__GCF_000276805.1:WP_017222136.1  75 LNWEFSKQALQDKLKLASLHIINDYTAISLAVPFLSAEEKIQIGAGECQTDGVTAVFGPGTGLGVSHIVK-AA 146
                                           *********************************************************************9.99 PP

                             TIGR00749 148 grykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelke 220
                                           g++ +l geGghv+f+P+ ++++ +l +l++++g+vsaer+lsG+Glv++y+ l      ++ +k+     ++
  NCBI__GCF_000276805.1:WP_017222136.1 147 GKWISLDGEGGHVSFTPNTPEQADILCLLQTQFGHVSAERILSGQGLVNLYKCLCTLS--EQEAKFD----QP 213
                                           ******************************************************9887..4456766....8* PP

                             TIGR00749 221 kdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlk 293
                                           kd+++aal+gs+ +ar++l +f+ ++G +agnlal+l   GG+y+aGGivPrf++++++s fr  fe+kGr+k
  NCBI__GCF_000276805.1:WP_017222136.1 214 KDVTKAALDGSCDIARKSLAVFCQVMGGFAGNLALNLACTGGIYIAGGIVPRFVDFFQASEFRRCFEEKGRFK 286
                                           ************************************************************************* PP

                             TIGR00749 294 ellasiPvqvvlkkkvGllGa 314
                                           ++l+ iP  ++ ++++GllGa
  NCBI__GCF_000276805.1:WP_017222136.1 287 DYLTAIPTFLITHDNPGLLGA 307
                                           ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (319 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 13.25
//
[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:

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:

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:

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:

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