GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Chryseobacterium arthrosphaerae CC-VM-7

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_065398804.1 BBI00_RS10955 aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_001684965.1:WP_065398804.1
          Length = 509

 Score =  236 bits (601), Expect = 2e-66
 Identities = 162/484 (33%), Positives = 255/484 (52%), Gaps = 17/484 (3%)

Query: 9   NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68
           NYI+G++      QY DVV+P   +   QV  S+KED++ A   AA+AF+TW   +   R
Sbjct: 24  NYIDGKFTPPVKGQYFDVVSPVDGKNFTQVAHSSKEDLELAVDAAAKAFQTWKNTSSTER 83

Query: 69  ARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMGDSL 127
           + IL      + Q+ E LA + TI+NGK  +E L  ++   I++  + A       G S 
Sbjct: 84  SIILNKIADRIEQNLEYLATVETIDNGKAVRETLAADLPLAIDHFRYFASVIRADEG-SH 142

Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187
             +  D  +     P+GV+  I P+NFP+++  W    A+A GN  +LKP+E TP+    
Sbjct: 143 NELDKDTVSLIVHEPLGVIAQIIPWNFPILMAVWKLAPALAAGNCVVLKPAESTPVSIMI 202

Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246
           L+EL     LP GV N+V G   ++   ++ +P++   +F GS   G  V +  +EN+  
Sbjct: 203 LMELIGDL-LPAGVINIVNGFGAELGRALVTNPKVAKAAFTGSTATGRLVMQYATENIIP 261

Query: 247 VQSLTGAKNHTIVLN---DANLEDTVTNIVGAAFG--SAGERCMACAVVTVEEGIADEFM 301
           V    G K+  +  N   DA+ E     I GA     + GE C   + + V+EGIAD F+
Sbjct: 262 VTLELGGKSPNVFFNSVMDADDEFLDKAIEGAVLFALNQGEICTCPSRLLVQEGIADAFI 321

Query: 302 AKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGREN----V 357
            K+ E+V  IK+GN LD  V +G    +  K + LSYI+ G++EGA ++  G  N     
Sbjct: 322 EKVIERVKAIKVGNPLDKTVMMGAQASKIQKDKILSYIQLGIDEGAEVLVGGDVNHLGED 381

Query: 358 SDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417
            +DG+++ PTIF      M I+++EIF PVL+    K+ +EA++IAN + +  GA ++T 
Sbjct: 382 LEDGFYIQPTIFKG-NNRMRIFQEEIFGPVLAFTTFKDEEEAVKIANDTMYGLGAGVWTR 440

Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477
           +++ +      I+AG + +N     P A  PF G+K S  G    N K  +D Y + K +
Sbjct: 441 DAHQLYNIPRQIEAGRVWVNQYHSYP-AGAPFGGYKQSGIG--RENHKMMLDHYRQTKNM 497

Query: 478 TARY 481
              Y
Sbjct: 498 LISY 501


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: 584
Number of extensions: 28
Number of successful extensions: 7
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: 509
Length adjustment: 34
Effective length of query: 453
Effective length of database: 475
Effective search space:   215175
Effective search space used:   215175
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