GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Stenotrophomonas chelatiphaga DSM 21508

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::V4GH04
         (496 letters)



>NCBI__GCF_001431535.1:WP_057507564.1
          Length = 501

 Score =  220 bits (560), Expect = 1e-61
 Identities = 156/490 (31%), Positives = 239/490 (48%), Gaps = 31/490 (6%)

Query: 16  QMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPP 75
           ++LI GQ++ + +    +V NPAT D+L +VP     +V+ AV  AAA     TWR+ P 
Sbjct: 9   RLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAV--AAAKEAFKTWRKTPI 66

Query: 76  SARERILLRLADLLEVHGDELARLETLNNGKLL------IYSKLMEVGASAQWLRYMAGW 129
             R RI L+   L+  +  ELA   +   GK +      ++  L  V  +A       G 
Sbjct: 67  GTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLGE 126

Query: 130 ATKLTGSTLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTV 189
                 + +D              T   P+GV A I P+NFP ++ +W    A+A GNT 
Sbjct: 127 LANNVANGVD------------TYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTF 174

Query: 190 VLKPAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEV 249
           VLKP+E+ P+  +RL ELA+EAG+P G LNVV G GE   +A+  HP +  V+F GST V
Sbjct: 175 VLKPSEQDPMVTMRLVELALEAGIPKGVLNVVHG-GEEVVNAICDHPDIKAVSFVGSTRV 233

Query: 250 GRIIGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYV 309
           G  + +    + K V   +G K+  +VL D + ++       A F   GQ C A S L V
Sbjct: 234 GTHVYNRASLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTL-V 292

Query: 310 HESIYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICG 369
                   +  L    +++ V +G   G  +GP++S    E V   I +G+E GA L   
Sbjct: 293 LVGEARSWVPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLD 352

Query: 370 GTEAPCAQGF----FVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSV 425
           G   P   GF    FV PTIF+     D+R+  +E+FGPVLV      + + +   N + 
Sbjct: 353 GRN-PQVDGFEKGNFVGPTIFSG-VTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNP 410

Query: 426 YGLGASIWTNDLSAALRINDELEAGTVWVNTHNMVD-PNLPFGGFKDSGVG--REHGAAA 482
            G G +++T   +AA +  ++++ G V +N    V  P   F G + S +G    +G   
Sbjct: 411 NGNGTAVFTQSGAAARKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLGDLGPYGKQV 470

Query: 483 IEHYTTTRSL 492
           +  YT T+++
Sbjct: 471 VMFYTQTKTI 480


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: 628
Number of extensions: 37
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 496
Length of database: 501
Length adjustment: 34
Effective length of query: 462
Effective length of database: 467
Effective search space:   215754
Effective search space used:   215754
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 Apr 09 2024. 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