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

GapMind for catabolism of small carbon sources

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

Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate CA265_RS07870 CA265_RS07870 glycerol kinase

Query= CharProtDB::CH_121461
         (502 letters)



>FitnessBrowser__Pedo557:CA265_RS07870
          Length = 496

 Score =  633 bits (1632), Expect = 0.0
 Identities = 305/492 (61%), Positives = 384/492 (78%), Gaps = 6/492 (1%)

Query: 5   KYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEV 64
           KYI+++DQGTTSSRA++ +H+  I++++QREF QIYPK GWVEHDPMEIW+TQ + + EV
Sbjct: 3   KYILSIDQGTTSSRAIIFNHNGEIVAIAQREFTQIYPKAGWVEHDPMEIWSTQLAVVTEV 62

Query: 65  LAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDY 124
           + KA ++   I +IGITNQRETT+VW+KETG+PIYNAIVWQ RRT+  C+ +K  GL   
Sbjct: 63  IVKAGLTVGDIDSIGITNQRETTVVWDKETGQPIYNAIVWQDRRTSAYCDEIKAQGLASK 122

Query: 125 IRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDY 184
           I+  TGL+ID YFS TK +WIL +V G+RE+A  G+L FGT+DTWLIWK+T G  HVTD 
Sbjct: 123 IQEKTGLIIDSYFSATKARWILQNVAGAREKAEAGKLAFGTIDTWLIWKLTAGEKHVTDV 182

Query: 185 TNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISGIA 244
           +NASRTML+NIHTL WDD++LE+  IP+ MLPEV+ SSEVYG+T  G     +IPI+GIA
Sbjct: 183 SNASRTMLYNIHTLSWDDELLELFSIPKAMLPEVKSSSEVYGET-AGRILAAKIPIAGIA 241

Query: 245 GDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALE 304
           GDQQ+ALFGQ+C + GM KNTYGTGCFMLMN G K   S N LLTTIA    GEVNYALE
Sbjct: 242 GDQQSALFGQMCTETGMVKNTYGTGCFMLMNIGSKPKISANNLLTTIAWQINGEVNYALE 301

Query: 305 GAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGA 364
           G++F+ GA +QWLRDEM LI+ + D E  A KV++T+GVYVVPAF GLGAP+WD +ARG 
Sbjct: 302 GSIFIGGAVVQWLRDEMGLISKSADVETLAKKVKDTDGVYVVPAFAGLGAPHWDQHARGT 361

Query: 365 IFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQS 424
           I GLTRG N +HI RA LESIAYQT DVL+AM+AD+G+ +  LRVDGGA AN+ LMQFQ+
Sbjct: 362 ITGLTRGTNKSHIARAALESIAYQTMDVLKAMEADAGVNIAELRVDGGATANDLLMQFQA 421

Query: 425 DILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREF--RPGIETTERNY 482
           D+L  +V RP+V EVTA+GAAYLAGLA GFW+++D+++ +  I R F    GI+ TE   
Sbjct: 422 DLLNCKVIRPDVTEVTAIGAAYLAGLATGFWKSIDQIRSQWKINRTFVAEEGIDNTE--- 478

Query: 483 RYAGWKKAVKRA 494
           R  GW +A+K A
Sbjct: 479 RIKGWNRAIKAA 490


Lambda     K      H
   0.318    0.134    0.404 

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: 743
Number of extensions: 23
Number of successful extensions: 2
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: 502
Length of database: 496
Length adjustment: 34
Effective length of query: 468
Effective length of database: 462
Effective search space:   216216
Effective search space used:   216216
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 CA265_RS07870 CA265_RS07870 (glycerol kinase)
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))

# 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/TIGR01311.hmm
# target sequence database:        /tmp/gapView.11304.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01311  [M=496]
Accession:   TIGR01311
Description: glycerol_kin: glycerol 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.6e-230  750.0  11.1   5.7e-230  749.7  11.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS07870  CA265_RS07870 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS07870  CA265_RS07870 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  749.7  11.1  5.7e-230  5.7e-230       1     493 [.       3     490 ..       3     492 .. 0.98

  Alignments for each domain:
  == domain 1  score: 749.7 bits;  conditional E-value: 5.7e-230
                                  TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleika 68 
                                                k+i++iDqGttssrai+f+++ge+va+aq+e++qi+pk+gwvEhdp+ei++++++v++e++ k++ ++
  lcl|FitnessBrowser__Pedo557:CA265_RS07870   3 KYILSIDQGTTSSRAIIFNHNGEIVAIAQREFTQIYPKAGWVEHDPMEIWSTQLAVVTEVIVKAGLTV 70 
                                                69****************************************************************** PP

                                  TIGR01311  69 eeiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsat 136
                                                 +i +iGitnqREttvvWdketg+p++naivWqd+rt+ +++e+k+++  ++++ektGL++++Yfsat
  lcl|FitnessBrowser__Pedo557:CA265_RS07870  71 GDIDSIGITNQRETTVVWDKETGQPIYNAIVWQDRRTSAYCDEIKAQGLASKIQEKTGLIIDSYFSAT 138
                                                ******************************************************************** PP

                                  TIGR01311 137 KlrWlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelf 204
                                                K rW+l+nv ++r++ae+g+l fGt+dtwli+kLt g++hvtdv+NASRt+l+n++tl+wd+ellelf
  lcl|FitnessBrowser__Pedo557:CA265_RS07870 139 KARWILQNVAGAREKAEAGKLAFGTIDTWLIWKLTAGEKHVTDVSNASRTMLYNIHTLSWDDELLELF 206
                                                ******************************************************************** PP

                                  TIGR01311 205 kipkellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllnt 272
                                                +ipk++lPe++sssevyge++ + +l +++pi+g++Gdqq+al+gq+c+++g++KntYgtGcF+l+n+
  lcl|FitnessBrowser__Pedo557:CA265_RS07870 207 SIPKAMLPEVKSSSEVYGETAGR-ILAAKIPIAGIAGDQQSALFGQMCTETGMVKNTYGTGCFMLMNI 273
                                                ********************988.******************************************** PP

                                  TIGR01311 273 GekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedseg 340
                                                G+k++is ++lLtt+a++++g+ +  yalEGs++++Ga+vqwlrd+++li+k+++ve+lak+v+d++g
  lcl|FitnessBrowser__Pedo557:CA265_RS07870 274 GSKPKISANNLLTTIAWQINGEVN--YALEGSIFIGGAVVQWLRDEMGLISKSADVETLAKKVKDTDG 339
                                                *********************985..****************************************** PP

                                  TIGR01311 341 vyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvD 408
                                                vy+VPaf+GL+aP+Wd++Argti+Gltr+t+k+hiaraale++a+q+ d+l+ame+dagv++++L+vD
  lcl|FitnessBrowser__Pedo557:CA265_RS07870 340 VYVVPAFAGLGAPHWDQHARGTITGLTRGTNKSHIARAALESIAYQTMDVLKAMEADAGVNIAELRVD 407
                                                ******************************************************************** PP

                                  TIGR01311 409 GglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemde 476
                                                Gg+++n+llmq+qad+l++kv rp v+e+ta+GaA++agla+g+wks ++++++++ + +tf +e   
  lcl|FitnessBrowser__Pedo557:CA265_RS07870 408 GGATANDLLMQFQADLLNCKVIRPDVTEVTAIGAAYLAGLATGFWKSIDQIRSQWKIN-RTFVAEEG- 473
                                                *********************************************************7.88887754. PP

                                  TIGR01311 477 eerekkykkwkeavers 493
                                                   ++++k w++a++ +
  lcl|FitnessBrowser__Pedo557:CA265_RS07870 474 IDNTERIKGWNRAIKAA 490
                                                455678999*9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (496 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: 7.73
//
[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