GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudarthrobacter sulfonivorans Ar51

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_001484605.1:WP_058929223.1
          Length = 508

 Score =  248 bits (632), Expect = 5e-70
 Identities = 152/478 (31%), Positives = 247/478 (51%), Gaps = 10/478 (2%)

Query: 5   RKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSK 62
           R     I+G WV+S + +    V+P       +VP +T ED+D A + A  AF    W +
Sbjct: 19  RSYSMLIDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWPQ 78

Query: 63  VAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLM 122
               +RA +L  F  LL+++ +ELA     ENGK   E      +  ++  + AG    +
Sbjct: 79  TLPSQRAALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMGQHAHYVAGLAETI 138

Query: 123 MGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTP 182
            G ++ S   +  A  +R PIGVV  I P+N P+M+  W    A+A GNT ++KPSE TP
Sbjct: 139 QGRTIESNWPNTAAFTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEATP 198

Query: 183 LLTEKLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGS 241
             T ++ EL  +AG P GV NVV G      + +++H  +  I+F GS   G  + K+ +
Sbjct: 199 TSTLRMAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGRAINKQAA 258

Query: 242 ENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFM 301
           E   RV    G K+  I+ +DA++++ V   +   FG+ G+ CM  + V V++ I D+F+
Sbjct: 259 ERFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGGSRVLVQDSIYDDFV 318

Query: 302 AKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS--- 358
            ++      + +G+ LD  V +GPV      ++ + Y++ G  EGA +V  G   ++   
Sbjct: 319 DRMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGARCMTTSE 378

Query: 359 -DDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417
              G F  PT+F NV+ E  + ++EIF PV S+IR ++  EA++IAN S+F   A ++T+
Sbjct: 379 LSKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFGLAAGVWTN 438

Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475
           + +        + +G + +N          PF G+K S  G     G D++D YT  K
Sbjct: 439 DVSRAHRMIRRVRSGTVWVNT-YRLTNYSVPFGGFKQSGIG--RELGPDALDAYTEVK 493


Lambda     K      H
   0.318    0.136    0.396 

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: 541
Number of extensions: 29
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: 487
Length of database: 508
Length adjustment: 34
Effective length of query: 453
Effective length of database: 474
Effective search space:   214722
Effective search space used:   214722
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