GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB 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)



>lcl|FitnessBrowser__Phaeo:GFF3251 PGA1_c33040 aldehyde
           dehydrogenase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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