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_008991223.1 I215_RS06780 glucosamine-6-phosphate deaminase

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



>NCBI__GCF_000300875.1:WP_008991223.1
          Length = 638

 Score =  748 bits (1932), Expect = 0.0
 Identities = 368/632 (58%), Positives = 466/632 (73%), Gaps = 7/632 (1%)

Query: 8   EETRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIAVYAELVR 67
           E+T+FEK+   +FE+   AS  VA  IA+LI+ KQ      VLGLATG +PI VY ELVR
Sbjct: 14  EDTKFEKIHNEIFEDSYEASKVVAAEIADLIRQKQDKGEACVLGLATGSSPIKVYEELVR 73

Query: 68  LHKEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIPDGTLALE 127
           LHK   LSF NVITFNLDEYYPM     QSY  FM+++LF+HIDI+ +N+HIP G ++ E
Sbjct: 74  LHKNGELSFHNVITFNLDEYYPMDAENRQSYYYFMHQHLFDHIDINPENIHIPSGQVSQE 133

Query: 128 DIPAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDLTRRDAAR 187
           ++  +C++Y+ KI  LGGLD Q+LGIGRTGHIGFNEPGS  NSGTR++TLD +TRRDAA 
Sbjct: 134 ELNQYCIDYDMKIKQLGGLDFQLLGIGRTGHIGFNEPGSHINSGTRIITLDHITRRDAAS 193

Query: 188 DFGGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPATFLQLSD 247
           DF G   VP KAITMG+ TI K++ II++AW  KKASIIK+ VEG+I+  +PA+FLQ   
Sbjct: 194 DFNGIENVPKKAITMGVSTILKSKRIIMLAWGHKKASIIKETVEGQITATIPASFLQNHP 253

Query: 248 HVEFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTEDDYNNNG 307
           +   I+D  AASEL+R  TPW+V  CVWTD L  KAV WL+  LKKP+LKLT+ DYN +G
Sbjct: 254 NTTMIMDQEAASELSRIKTPWIVSQCVWTDNLKLKAVTWLSEELKKPVLKLTDKDYNEHG 313

Query: 308 MAQLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVIIFSPHPD 367
           M+ L + +G  YN+NI IFNKLQHTITGWPGGKPNADD+ RPER  P KKR+IIFSPHPD
Sbjct: 314 MSGLLSIEGSSYNLNIKIFNKLQHTITGWPGGKPNADDTNRPERKSPEKKRIIIFSPHPD 373

Query: 368 DDVISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKMGMDNTHLKD 427
           DDVISMGGTF RL++QGHDVHVAYQTSGN AV D++AL+F E  V        + T+ K 
Sbjct: 374 DDVISMGGTFSRLIEQGHDVHVAYQTSGNIAVTDEEALKFAE--VANLLSPSTEETNFK- 430

Query: 428 LYNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQALPFYESGK 487
              K+ +F+  K     D+ E + VKGLIR+ E+    RY GL+D  +HF  LPFYE+G+
Sbjct: 431 ---KIISFLNSKTTAYGDSLETRKVKGLIRRMESYGATRYLGLDDSKVHFLDLPFYETGE 487

Query: 488 VQKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRLRKTEAWA 547
           V+KNPV   DI+L  +L+  ++P Q+YAAGD  DPHGTH +C + I E+L  ++  + + 
Sbjct: 488 VKKNPVGPEDIQLISDLITTIQPHQIYAAGDLADPHGTHKLCLDAIFESLASIKHLD-FM 546

Query: 548 QDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGDDSREFWQ 607
            DCW+W+YRGAWHE++  +IEMAVP+SP E+ +K  AI  HQSQKDR +F G+DSREFW 
Sbjct: 547 DDCWVWLYRGAWHEWDIADIEMAVPLSPDEMNKKINAILFHQSQKDRVMFQGEDSREFWV 606

Query: 608 RAEDRNRDTAKAYDELGLAEYEAMEAFVRWKF 639
           RA++RNR+TA  YD LGLAEYEA+EAF R+ F
Sbjct: 607 RAQERNRNTALLYDNLGLAEYEAIEAFKRYHF 638


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: 1128
Number of extensions: 33
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: 638
Length adjustment: 38
Effective length of query: 603
Effective length of database: 600
Effective search space:   361800
Effective search space used:   361800
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_008991223.1 I215_RS06780 (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.3409792.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      3e-88  281.5   0.3    5.2e-88  280.7   0.3    1.3  1  NCBI__GCF_000300875.1:WP_008991223.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000300875.1:WP_008991223.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.7   0.3   5.2e-88   5.2e-88      10     248 ..      30     268 ..      24     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: 280.7 bits;  conditional E-value: 5.2e-88
                             TIGR00502  10 eelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvglseehP 82 
                                            e sk+ a+ ia+ i++ k+d+ +  vlGlatG++P+++y++l++l+k+g++sf++v+tfnldey  ++ e+ 
  NCBI__GCF_000300875.1:WP_008991223.1  30 YEASKVVAAEIADLIRQ-KQDKGEACVLGLATGSSPIKVYEELVRLHKNGELSFHNVITFNLDEYYPMDAENR 101
                                           57899************.999999************************************************* PP

                             TIGR00502  83 esyhsfmyenffqhidikpeninilnGnad..dleaecrryeekikslGkidlfllGiGadGhiafnePgssl 153
                                           +sy++fm++++f+hidi+peni+i+ G+ +  +l++ c  y+ kik+lG++d +llGiG+ Ghi+fnePgs +
  NCBI__GCF_000300875.1:WP_008991223.1 102 QSYYYFMHQHLFDHIDINPENIHIPSGQVSqeELNQYCIDYDMKIKQLGGLDFQLLGIGRTGHIGFNEPGSHI 174
                                           ***************************8651168899************************************ PP

                             TIGR00502 154 esrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvnedvti 226
                                           +s tr+ tl + t+   +  f+  +++vPkka+t+G+ til+sk++++l+ G++ka+ +k+ veg+++ ++++
  NCBI__GCF_000300875.1:WP_008991223.1 175 NSGTRIITLDHITRRDAASDFN-GIENVPKKAITMGVSTILKSKRIIMLAWGHKKASIIKETVEGQITATIPA 246
                                           **************99998898.7************************************************* PP

                             TIGR00502 227 salqlhkkvivvadeeaaqelk 248
                                           s lq h + ++++d+eaa+el 
  NCBI__GCF_000300875.1:WP_008991223.1 247 SFLQNHPNTTMIMDQEAASELS 268
                                           ******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (638 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 43.24
//
[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