GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Bacillus altitudinis 41KF2b

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_019744147.1 BA79_RS03900 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::V4GH04
         (496 letters)



>NCBI__GCF_000691145.1:WP_019744147.1
          Length = 486

 Score =  291 bits (745), Expect = 4e-83
 Identities = 178/489 (36%), Positives = 272/489 (55%), Gaps = 27/489 (5%)

Query: 19  IGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPSAR 78
           IGGQWV A++ +T  VYNPATG+++ EVP     DV  AV++A       TW +     R
Sbjct: 13  IGGQWVDAETNQTEAVYNPATGEVIAEVPLSTKTDVEHAVQAAQEAFT--TWSKTAVPRR 70

Query: 79  ERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGSTL 138
            RIL +   LL    DELA L TL NGK +  +K  EV    + + + AG  T + G  L
Sbjct: 71  ARILFKYQQLLVEKWDELAELVTLENGKSVTEAK-GEVQRGIECVEFAAGAPTLMMGKQL 129

Query: 139 DLSLPLPPEVRS--RASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEE 196
                  P++ +   +   R P+GV+  I P+NFP+++  W    A+ACGNT VLKP+E 
Sbjct: 130 -------PDIATGLESGMYRYPIGVIGGITPFNFPMMVPCWMFPLAIACGNTFVLKPSER 182

Query: 197 TPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRII--- 253
           TP+ A RLAEL  EAGLP G LN+V G  +   + L+ H KV  ++F GS  V   +   
Sbjct: 183 TPILAARLAELFEEAGLPKGVLNIVNGAHDVV-NGLLEHEKVKAISFVGSQPVAEYVYKK 241

Query: 254 GSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESI 313
           G+A G+ ++A++   G K+  IVL D D + A +    A F + G+ C A + + V E +
Sbjct: 242 GTAHGKRVQALA---GAKNHSIVLKDADLESATKQIIGAAFGSAGERCMAAAVVAVEEDV 298

Query: 314 YEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTE- 372
            +D+IQ+L      +V+G+G+ + V +GP++ K+H E  L++I++GIE+GA LI  G + 
Sbjct: 299 ADDLIQQLVDESNQLVIGNGINKDVFLGPVIRKEHKERTLQYIQSGIEEGASLIRDGRQD 358

Query: 373 -APCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGAS 431
                +G+FV PTIF +     +++   E+F PVL     S +AE ++ +N+S +  GA 
Sbjct: 359 NETNGEGYFVGPTIF-DHVTNQMKIWQDEIFAPVLSIVRVSSLAEAIDLSNQSKFANGAC 417

Query: 432 IWTNDLSAALRINDELEAGTVWVNTHNMVDPN--LPFGGFKDSGVGREH--GAAAIEHYT 487
           ++T+  S+     + +EAG + +N   +  P    PF G+KDS  G  H  G   +E YT
Sbjct: 418 LYTDSASSIREFRENIEAGMLGINI-GVPAPMAFFPFSGWKDSFYGDLHANGTDGVEFYT 476

Query: 488 TTRSLVIAY 496
             + +   Y
Sbjct: 477 RKKMVTARY 485


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: 583
Number of extensions: 33
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: 486
Length adjustment: 34
Effective length of query: 462
Effective length of database: 452
Effective search space:   208824
Effective search space used:   208824
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 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