GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Streptomyces kebangsaanensis SUK12

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein

Query= BRENDA::V4GH04
         (496 letters)



>NCBI__GCF_001906585.1:WP_073948994.1
          Length = 462

 Score =  333 bits (854), Expect = 8e-96
 Identities = 197/477 (41%), Positives = 262/477 (54%), Gaps = 24/477 (5%)

Query: 17  MLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPS 76
           M I G W  A     + V NPA   ++  VP G  EDV+AAV +A A L    W   PP+
Sbjct: 7   MYIDGAWRPAAGRDAIEVVNPADEQVIATVPAGTAEDVDAAVRAARAALPG--WAATPPA 64

Query: 77  ARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGS 136
            R   L  L D+L    DE+A   T   G  L +S+ +            AG    + GS
Sbjct: 65  ERAARLTALRDVLVARKDEIAETVTAELGSPLAFSQAVH-----------AGVPIAVAGS 113

Query: 137 TLDLSLPLPPEVRSRAST-QRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAE 195
             DL+     E +   ST    PVGVV AI PWN+PL   V K APALA G T+VLKPAE
Sbjct: 114 YADLAATYAFEEKVGNSTVHHEPVGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAE 173

Query: 196 ETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGS 255
           +TPLTA   AE A EAG+PAG LN+VTG G  AG AL  HP V  V+FTGST VGR IG+
Sbjct: 174 DTPLTAQLFAEAAHEAGIPAGVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVGRRIGA 233

Query: 256 ACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYE 315
             G ++K V+LELGGKS  ++L   D   A     A +  N GQ C+A +R+ VH   Y+
Sbjct: 234 TAGAAVKRVALELGGKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYD 293

Query: 316 DVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPC 375
           + ++  A         +  + G  +GP+V+ K    V  +I  GI +GA L+ GG EAPC
Sbjct: 294 EAVELAAT--------AAAKYGDRIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPEAPC 345

Query: 376 AQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTN 435
            +G+FV PT+FA+    D+ +  +E+FGPVL    + D  + +  AN +VYGL  ++W  
Sbjct: 346 EKGYFVSPTVFAD-VTPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVWAA 404

Query: 436 DLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSL 492
           D + A+     ++ G V +N     +P  PFGG+K SGVGRE GA  +  Y  T+SL
Sbjct: 405 DETEAVAFARRMDTGQVDIN-GGRFNPLAPFGGYKQSGVGRELGAHGLTEYLQTKSL 460


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: 576
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: 496
Length of database: 462
Length adjustment: 34
Effective length of query: 462
Effective length of database: 428
Effective search space:   197736
Effective search space used:   197736
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: 51 (24.3 bits)

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