GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Phaeobacter inhibens BS107

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC

Query= BRENDA::V4GH04
         (496 letters)



>lcl|FitnessBrowser__Phaeo:GFF3174 PGA1_c32250
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
           PuuC
          Length = 494

 Score =  317 bits (811), Expect = 8e-91
 Identities = 190/477 (39%), Positives = 263/477 (55%), Gaps = 10/477 (2%)

Query: 18  LIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPSA 77
           LI GQ V+A  G T++V +P  G +LT++  G V D+  A+ SA A      W   PP+A
Sbjct: 20  LIDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAFEDRRWAGQPPAA 79

Query: 78  RERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGST 137
           R+++L++ A+L+E     LA L   +NG  +  +   E G++A  +RY A    K+ G  
Sbjct: 80  RKKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGSAAATIRYYAEALDKIYGEI 139

Query: 138 LDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEET 197
              S  +   V         PVGVV AIIPWNFP+++  WK+APALA GN+VVLKP+E  
Sbjct: 140 APTSSDVLGMVHKE------PVGVVGAIIPWNFPMMIGAWKLAPALAMGNSVVLKPSETA 193

Query: 198 PLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGSAC 257
            L+ +R+ ELA+EAGLP G LN VTG G   G+AL     V  + FTGS + GR +    
Sbjct: 194 SLSLMRMVELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGSGQTGRRLMEYA 253

Query: 258 GRS-LKAVSLELGGKSPVIVLADC-DPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYE 315
            RS LK V LELGGKSP IV AD  D  +AA+  AA IF N GQVC AGSRL V  SI++
Sbjct: 254 ARSNLKRVYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAGSRLLVEASIHD 313

Query: 316 DVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPC 375
             ++ +A   + + VG  L     +G + S+      L+ +     +G  +I GG     
Sbjct: 314 AFVEEVAKAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGGQIITGGQRLLS 373

Query: 376 -AQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWT 434
              G ++ PTI       D  L  +EVFGPVL  TPF   AE +  AN +VYGL  ++WT
Sbjct: 374 ETGGSYMAPTIVTG-VTPDATLAQEEVFGPVLAVTPFETDAEALRIANATVYGLAGAVWT 432

Query: 435 NDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRS 491
           + L+ A R+   +  G + VNT+   D  +P GG   SG G +    AI+ Y   ++
Sbjct: 433 SGLTRAHRMVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHAIDKYINLKT 489


Lambda     K      H
   0.317    0.134    0.395 

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: 595
Number of extensions: 27
Number of successful extensions: 5
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: 496
Length of database: 494
Length adjustment: 34
Effective length of query: 462
Effective length of database: 460
Effective search space:   212520
Effective search space used:   212520
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)

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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