GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Galbibacter marinus ck-I2-15

Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate WP_008992130.1 I215_RS11450 glucosamine-6-phosphate deaminase

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



>NCBI__GCF_000300875.1:WP_008992130.1
          Length = 644

 Score =  751 bits (1940), Expect = 0.0
 Identities = 362/632 (57%), Positives = 468/632 (74%), Gaps = 6/632 (0%)

Query: 8   EETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIAVYAELVR 67
           E+ R+EK+   VFE+   AS+ VA  IA+LI  K       VLGLATG +PI VY ELV+
Sbjct: 19  EDNRYEKIHNVVFESSSEASLLVAREIADLIVDKNNRGETCVLGLATGSSPIRVYDELVK 78

Query: 68  LHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIPDGTLALE 127
           +H+E GLSFKNV++FNLDEY+PM P +  SY  FMNE+LFNHIDI K+N+ IPDGT+A +
Sbjct: 79  MHRENGLSFKNVVSFNLDEYFPMNPESIHSYHHFMNEHLFNHIDIPKENIFIPDGTIAQQ 138

Query: 128 DIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDLTRRDAAR 187
           DIPA+C  YE+KI   GG+D Q+LGIGRTGHIGFNEPGS  NS TR +TLD LTR DA+ 
Sbjct: 139 DIPAYCQGYEQKIKSFGGIDFQLLGIGRTGHIGFNEPGSHYNSITRSITLDQLTREDASS 198

Query: 188 DFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPATFLQLSD 247
            F G   VP KAITMG+GT+F A+ I+L+AW  KKA ++K+ +EGEI   +PAT+LQ   
Sbjct: 199 GFHGIENVPKKAITMGVGTVFSAKRIVLLAWGHKKAEVVKQTIEGEILPQIPATYLQEHL 258

Query: 248 HVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTEDDYNNNG 307
           +   +L+  AAS LTRF +PWLV +  W++AL+++AV+WL   + K IL+LT+ DYN +G
Sbjct: 259 NTTMVLNTEAASMLTRFESPWLVGEVQWSEALMKRAVVWLCRKVDKSILRLTDKDYNEHG 318

Query: 308 MAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVIIFSPHPD 367
           +A L TEKG  Y +NI +FNKLQHTITGWPGGKPNADDS RPER  P KKRVIIFSPHPD
Sbjct: 319 LASLITEKGSTYQLNIDMFNKLQHTITGWPGGKPNADDSNRPERKSPEKKRVIIFSPHPD 378

Query: 368 DDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGMDNTHLKD 427
           DDVISMGGTF RLV+QGH+VH+AYQTSGN AV + DAL+F E  +DF     + N    D
Sbjct: 379 DDVISMGGTFDRLVEQGHEVHIAYQTSGNIAVSNADALKFAEVAMDF-----LPNCKGVD 433

Query: 428 LYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQALPFYESGK 487
              K    IE ++ N+ID  E++ +KGLIRK E+IA  RY  + D+ +HF  LPFYE+G 
Sbjct: 434 KLQKATKAIEDQRENEIDPLEVRELKGLIRKRESIAATRYLNVPDEQVHFLNLPFYETGT 493

Query: 488 VQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRLRKTEAWA 547
           ++KNP++  DI +  +L+  ++P QVYAAGD  DPHGTH VC + + +A+  L K++++ 
Sbjct: 494 IKKNPLSQDDIAIVKKLISDIQPHQVYAAGDLADPHGTHKVCLDAVFKAMAEL-KSQSYM 552

Query: 548 QDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGDDSREFWQ 607
             CWLW+YRGAWHE+E HEI+MAVP+SP ++ RK+ AIF HQSQKD  +F G+D REFW 
Sbjct: 553 DQCWLWLYRGAWHEWEIHEIDMAVPMSPDQVLRKRKAIFFHQSQKDGVLFQGEDLREFWV 612

Query: 608 RAEDRNRDTAKAYDELGLAEYEAMEAFVRWKF 639
           RAE+RN++TAK Y +LGLA+Y A+EAF R+ +
Sbjct: 613 RAEERNKETAKHYRDLGLADYAAIEAFKRFDY 644


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: 1163
Number of extensions: 40
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: 641
Length of database: 644
Length adjustment: 38
Effective length of query: 603
Effective length of database: 606
Effective search space:   365418
Effective search space used:   365418
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 WP_008992130.1 I215_RS11450 (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.1821462.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-81  259.7   0.1    2.1e-81  259.1   0.1    1.2  1  NCBI__GCF_000300875.1:WP_008992130.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000300875.1:WP_008992130.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.1   0.1   2.1e-81   2.1e-81       7     247 ..      32     272 ..      26     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: 259.1 bits;  conditional E-value: 2.1e-81
                             TIGR00502   7 etyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvglse 79 
                                           e   e s l ar ia+ i + k+++ +  vlGlatG++P+ +y +l+++++ + +sfk+vv fnldey  +++
  NCBI__GCF_000300875.1:WP_008992130.1  32 ESSSEASLLVAREIADLIVD-KNNRGETCVLGLATGSSPIRVYDELVKMHRENGLSFKNVVSFNLDEYFPMNP 103
                                           567788999***********.888899********************************************** PP

                             TIGR00502  80 ehPesyhsfmyenffqhidikpeninilnGn..addleaecrryeekikslGkidlfllGiGadGhiafnePg 150
                                           e  +syh+fm+e++f+hidi +eni+i++G   ++d+ a c+ ye+kiks+G+id +llGiG+ Ghi+fnePg
  NCBI__GCF_000300875.1:WP_008992130.1 104 ESIHSYHHFMNEHLFNHIDIPKENIFIPDGTiaQQDIPAYCQGYEQKIKSFGGIDFQLLGIGRTGHIGFNEPG 176
                                           ******************************73256788*********************************** PP

                             TIGR00502 151 sslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvned 223
                                           s ++s tr  tl + t+   s  f+  +++vPkka+t+G++t++++k+++ll+ G++kae vk+ +eg +  +
  NCBI__GCF_000300875.1:WP_008992130.1 177 SHYNSITRSITLDQLTREDASSGFH-GIENVPKKAITMGVGTVFSAKRIVLLAWGHKKAEVVKQTIEGEILPQ 248
                                           *****************98888887.6********************************************** PP

                             TIGR00502 224 vtisalqlhkkvivvadeeaaqel 247
                                           ++++ lq h + ++v ++eaa+ l
  NCBI__GCF_000300875.1:WP_008992130.1 249 IPATYLQEHLNTTMVLNTEAASML 272
                                           *******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (644 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: 20.89
//
[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