Alignments for a candidate for gntK in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gntK in Herbaspirillum seropedicae SmR1

Align Gluconokinase; EC 2.7.1.12; Gluconate kinase (uncharacterized)
to candidate HSERO_RS05475 HSERO_RS05475 gluconokinase

Query= curated2:P46834
         (513 letters)



>FitnessBrowser__HerbieS:HSERO_RS05475
          Length = 520

 Score =  582 bits (1499), Expect = e-170
 Identities = 279/509 (54%), Positives = 379/509 (74%), Gaps = 3/509 (0%)

Query: 1   MTSYMLGIDIGTTSTKAVLFSEKGDVIQKESIGYALYTPDISTAEQNPDEIFQAVIQSTA 60
           +  YMLG+DIGTTSTK+V+F+  G V+ + +  Y +   +   AEQ+P++I  A + S A
Sbjct: 6   LARYMLGVDIGTTSTKSVVFTLDGKVVAQHAEEYPVLCTEPGMAEQDPEQIVAAALASIA 65

Query: 61  KIMQ--QHPDKQPSFISFSSAMHSVIAMDENDKPLTSCITWADNRSEGWAHKIKEEMNGH 118
             ++  +   ++ + +SFS+AMHSVIA+D  ++ L++ ITW D R+  WA +IK E +G+
Sbjct: 66  GAVKAAKAAPQEIALLSFSAAMHSVIALDAENRLLSNSITWGDIRASVWAERIKHEHDGN 125

Query: 119 NVYKRTGTPIHPMAPLSKITWIVNEHPEIAVKAKKYIGIKEYIFKKLFDQYVVDYSLASA 178
            +Y+RTGTP+HPM+PL K+ W+ +E P++  +A +++GIKEY+  +LF Q+VVD+S+ASA
Sbjct: 126 AIYRRTGTPVHPMSPLCKLMWMRHEKPDVFHRAARFVGIKEYLLYQLFGQWVVDHSIASA 185

Query: 179 MGMMNLKTLAWDEEALAIAGITPDHLSKLVPTTAIFHHCNPELAAMMGIDPQTPFVIGAS 238
            GM NL+ LAWD+ ALA+ G+ PD L   VPTT      + E+A  +G+   TPF+IGA+
Sbjct: 186 TGMFNLRELAWDQGALALLGVRPDQLPTPVPTTHRLPALSSEMAQRLGLSVDTPFIIGAN 245

Query: 239 DGVLSNLGVNAIKKGEIAVTIGTSGAIRPIIDKPQTDEKGRIFCYALTENHWVIGGPVNN 298
           DGVLSNLGVNAI+ G +AVTIGTSGA+R +ID+P+TD +GR+FCYALTE HWV+GGPVNN
Sbjct: 246 DGVLSNLGVNAIEIGHVAVTIGTSGAMRTVIDEPRTDPQGRLFCYALTEKHWVVGGPVNN 305

Query: 299 GGIVLRWIRDEFASSEIETAKRLGIDPYDVLTKIAERVRPGADGLLFHPYLAGERAPLWN 358
           GG + RW+RDE A++E   A+  G+DPY+ LT+IAE+VRPGA+GLLFHP++AGERAPLWN
Sbjct: 306 GGNIFRWVRDELATAEAAAAREEGVDPYEALTRIAEKVRPGAEGLLFHPFMAGERAPLWN 365

Query: 359 PDVPGSFFGLTMSHKKEHMIRAALEGVIYNLYTVFLALTECMDGPVARIQATGGFARSDV 418
            D+ GSFFGL + H K HMIRAALEGVI+NLY++  AL E + GP  R+ ATGGFARS +
Sbjct: 366 ADLRGSFFGLALHHGKHHMIRAALEGVIFNLYSILPALEELV-GPTKRMMATGGFARSAL 424

Query: 419 WRQMMADIFESEVVVPESYESSCLGACILGLYATGKIDSFDVVSDMIGSTHRHAPKEESA 478
           WRQMMADIF  EVVVPES ESSCLGA +LG +A G + S  V+S M+GST+ HAP+ E+ 
Sbjct: 425 WRQMMADIFNREVVVPESVESSCLGAAVLGAWALGLVPSLSVISGMVGSTNHHAPEAEAV 484

Query: 479 KEYRKLMPLFINLSRALENEYTQIANYQR 507
             Y +L P+F  +   LE EY  IA +QR
Sbjct: 485 AVYGRLQPIFAAIPAKLEAEYHAIAAFQR 513


Lambda     K      H
   0.318    0.134    0.401 

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: 702
Number of extensions: 14
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: 513
Length of database: 520
Length adjustment: 35
Effective length of query: 478
Effective length of database: 485
Effective search space:   231830
Effective search space used:   231830
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: 52 (24.6 bits)

Align candidate HSERO_RS05475 HSERO_RS05475 (gluconokinase)
to HMM TIGR01314 (gntK: gluconate kinase (EC 2.7.1.12))

# 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/TIGR01314.hmm
# target sequence database:        /tmp/gapView.27905.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01314  [M=505]
Accession:   TIGR01314
Description: gntK_FGGY: gluconate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   9.2e-223  726.2   0.0     1e-222  726.0   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05475  HSERO_RS05475 gluconokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05475  HSERO_RS05475 gluconokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  726.0   0.0    1e-222    1e-222       1     505 []       9     513 ..       9     513 .. 0.99

  Alignments for each domain:
  == domain 1  score: 726.0 bits;  conditional E-value: 1e-222
                                  TIGR01314   1 yligvdigttstkavlfeengkvvakesigyplytddvdvaeenleeifeavlvtikevskele.eek 67 
                                                y++gvdigttstk+v+f  +gkvva++   yp+   + ++ae+++e+i  a l +i+  +k  +   +
  lcl|FitnessBrowser__HerbieS:HSERO_RS05475   9 YMLGVDIGTTSTKSVVFTLDGKVVAQHAEEYPVLCTEPGMAEQDPEQIVAAALASIAGAVKAAKaAPQ 76 
                                                9*******************************************************987766651567 PP

                                  TIGR01314  68 eikfvsfsaqmhslialdendkpltrlitwadnraakyaekikeekngfeiykrtgtpihpmaplski 135
                                                ei ++sfsa+mhs+iald +++ l++ itw d ra  +ae+ik+e++g++iy+rtgtp+hpm+pl+k+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05475  77 EIALLSFSAAMHSVIALDAENRLLSNSITWGDIRASVWAERIKHEHDGNAIYRRTGTPVHPMSPLCKL 144
                                                8******************************************************************* PP

                                  TIGR01314 136 iwlkaerkdifqkaakyleikeyifkrlfdtyvidyslasatgllnlkeldwdkealelagikeeqlp 203
                                                +w+++e++d+f++aa++++ikey++++lf+++v+d+s+asatg++nl+el wd+ al l+g++++qlp
  lcl|FitnessBrowser__HerbieS:HSERO_RS05475 145 MWMRHEKPDVFHRAARFVGIKEYLLYQLFGQWVVDHSIASATGMFNLRELAWDQGALALLGVRPDQLP 212
                                                ******************************************************************** PP

                                  TIGR01314 204 klvetteilknlkeeyakkmgidketkfvigasdgvlsnlgvnaikkgevavtigtsgairtvidkpk 271
                                                  v+tt+ l  l++e+a+++g+  +t+f+iga dgvlsnlgvnai+ g vavtigtsga+rtvid p+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05475 213 TPVPTTHRLPALSSEMAQRLGLSVDTPFIIGANDGVLSNLGVNAIEIGHVAVTIGTSGAMRTVIDEPR 280
                                                ******************************************************************** PP

                                  TIGR01314 272 tdekgrifcyalteehyviggpvnnggvvlrwlrdellaseietakrlgvdpydvltkiakrvkpgad 339
                                                td +gr+fcyalte+h+v+ggpvnngg ++rw+rdel+++e  +a+  gvdpy+ lt+ia++v+pga+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05475 281 TDPQGRLFCYALTEKHWVVGGPVNNGGNIFRWVRDELATAEAAAAREEGVDPYEALTRIAEKVRPGAE 348
                                                ******************************************************************** PP

                                  TIGR01314 340 gllfhpylageraplwnanargsffgltlshkkehmiraalegviynlytvalalvevvdetlkmika 407
                                                gllfhp++ageraplwna+ rgsffgl+l h k+hmiraalegvi+nly +  al e+v+  +k++ a
  lcl|FitnessBrowser__HerbieS:HSERO_RS05475 349 GLLFHPFMAGERAPLWNADLRGSFFGLALHHGKHHMIRAALEGVIFNLYSILPALEELVGP-TKRMMA 415
                                                *********************************************************9987.78889* PP

                                  TIGR01314 408 tggfaksevwrqllsdifesevvvpesyessclgaiilglkavgkiedlsavssmvgaterytpieen 475
                                                tggfa+s +wrq+++dif++evvvpes essclga +lg  a+g + +ls++s mvg+t+++ p  e+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05475 416 TGGFARSALWRQMMADIFNREVVVPESVESSCLGAAVLGAWALGLVPSLSVISGMVGSTNHHAPEAEA 483
                                                ******************************************************************** PP

                                  TIGR01314 476 vkvyreivpifinlsrsleeeyeqiadfqr 505
                                                v vy  + pif  +   le+ey+ ia fqr
  lcl|FitnessBrowser__HerbieS:HSERO_RS05475 484 VAVYGRLQPIFAAIPAKLEAEYHAIAAFQR 513
                                                *****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (505 nodes)
Target sequences:                          1  (520 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.30
//
[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