GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Shewanella sp. ANA-3

Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::O06837
         (502 letters)



>lcl|FitnessBrowser__ANA3:7025944 Shewana3_3092 succinate
           semialdehyde dehydrogenase (RefSeq)
          Length = 482

 Score =  305 bits (782), Expect = 2e-87
 Identities = 180/474 (37%), Positives = 261/474 (55%), Gaps = 10/474 (2%)

Query: 19  LPHQMLIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRR 78
           L  Q  I GQW +AQS +T+ + NPATG  +  VP     +  AA+ +A A L   AWR 
Sbjct: 9   LRQQCYINGQWCDAQSKETVAIANPATGAVIASVPVMGQAETQAAIAAAEAALP--AWRA 66

Query: 79  MPPSARERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATK 138
           +    R   L R  +LL  + D+LA + T   GK L  +K  EV  +A ++ + A  A +
Sbjct: 67  LTAKERGVKLRRWFELLNENSDDLALMMTSEQGKPLAEAKG-EVTYAASFIEWFAEEAKR 125

Query: 139 LTGSTLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLK 198
           + G T+            R    + PVGV AAI PWNFP  M   K APALA G T+V+K
Sbjct: 126 VYGDTIP-----GHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK 180

Query: 199 PAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRI 258
           PA +TP TAL LA LA  AG+PAG  +V+TG     G+ +  +P V K++FTGST+VG  
Sbjct: 181 PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIK 240

Query: 259 IGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHES 318
           +   C  +LK +SLELGG +P IV  D +   A EGA  A + N GQ C   +R+YV   
Sbjct: 241 LMEQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300

Query: 319 IYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTE 378
           +Y++  ++L++    + VG G+ +GV  GP+++    E V  H+ + +  GA ++ GG  
Sbjct: 301 VYDEFARKLSIAVGKLKVGEGIGEGVTTGPLINCAAVEKVQSHLEDALSKGATVVAGGKP 360

Query: 379 APCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASI 438
                 FF +PT+  N +   +R+  +E FGP+     F+D+ +V+ +AN + +GL A  
Sbjct: 361 HSLGGNFF-EPTVLTNVD-SSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYF 418

Query: 439 WTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHY 492
           +  D+S   ++ + LE G V VNT  +     PFGG K SG+GRE     IE Y
Sbjct: 419 YGRDISLVWKVTEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKFGIEEY 472


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: 534
Number of extensions: 29
Number of successful extensions: 4
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: 502
Length of database: 482
Length adjustment: 34
Effective length of query: 468
Effective length of database: 448
Effective search space:   209664
Effective search space used:   209664
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 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