GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Phaeobacter inhibens BS107

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF3251 PGA1_c33040 aldehyde dehydrogenase

Query= metacyc::MONOMER-13361
         (500 letters)



>FitnessBrowser__Phaeo:GFF3251
          Length = 479

 Score =  287 bits (734), Expect = 7e-82
 Identities = 174/475 (36%), Positives = 264/475 (55%), Gaps = 16/475 (3%)

Query: 23  YIDGNFVTSAS--SFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDR 80
           YI+G +V  A+   F  I+P      + +   DA   N AV AA+ AL G W    V++R
Sbjct: 8   YINGQWVAPAAPNDFEVIDPSTEAPCAVISLGDAADTNAAVAAAKTALPG-WMTTPVEER 66

Query: 81  AALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLF 140
            AL+ K+ +  ++R E+   A   + G P+  ART        + R F   AK      F
Sbjct: 67  IALVEKLIEVYESRTEDLAQAMSVEMGAPIDMARTQQAGAGSWHLRNFIKAAKA-----F 121

Query: 141 EMSTSDGSGALN-YTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPS 199
                 G  A N   + + +GV  +I+PWN P+   T KV  A   G T+V KPSE+SP 
Sbjct: 122 SFDAPLGDHAPNDRIIHEAVGVAALITPWNWPMNQVTLKVGAAAIAGCTMVLKPSEQSPL 181

Query: 200 SATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVA 259
           +A + AE+M +AG P GVFNL++G G    G  L+ HP +  ++FTG ++ G+ I KA A
Sbjct: 182 NAMIFAEMMDEAGFPAGVFNLVNGDG-TGVGTQLSSHPDVDMVSFTGSTRAGTAISKAAA 240

Query: 260 DGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFV 319
           D +K+V  ELGGK A V+F DAD  A   GVL     N+GQ C    R+ V + I+D+ V
Sbjct: 241 DTLKKVHLELGGKGANVIFDDADEKAVKRGVLH-MMNNTGQSCNAPSRMLVQKGIYDKAV 299

Query: 320 SGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGG-GVPKFND 378
                 A ++ VG    +G ++GP+++     K+    +  +DEGA +V GG G P   D
Sbjct: 300 EEAAAVANKVEVGPASSEGRHIGPVVNELQWGKIQDLIQKGIDEGARLVAGGTGRP---D 356

Query: 379 ERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWT 438
             +QG YV+PT++  ++++     EEIFGPV  I PF+ E++ I   ND+ YGL   + T
Sbjct: 357 GLNQGFYVKPTVFADVNNQMTIAREEIFGPVLSIIPFESEEDAIEIANDTPYGLTNYVQT 416

Query: 439 TNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDI 493
            +L+RA+R++R++  G++ +N    R   +PFGG+K SG GREGG + ++ + ++
Sbjct: 417 QDLARANRMARKLRAGMIEMN-GKSRSAGSPFGGMKQSGNGREGGSWGIEDFLEV 470


Lambda     K      H
   0.318    0.135    0.405 

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: 542
Number of extensions: 29
Number of successful extensions: 6
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: 500
Length of database: 479
Length adjustment: 34
Effective length of query: 466
Effective length of database: 445
Effective search space:   207370
Effective search space used:   207370
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 (21.7 bits)
S2: 52 (24.6 bits)

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:

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