GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Shewanella loihica PV-4

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 5209456 Shew_1927 dihydrolipoamide acetyltransferase (RefSeq)

Query= reanno::Marino:GFF1672
         (378 letters)



>FitnessBrowser__PV4:5209456
          Length = 520

 Score =  367 bits (942), Expect = e-106
 Identities = 198/377 (52%), Positives = 255/377 (67%), Gaps = 5/377 (1%)

Query: 1   MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60
           MTDKA+V+I A K+G+V KL++++  +A+VH PLF+      E    A       A +  
Sbjct: 148 MTDKALVQIPAIKSGKVVKLHYRKGQLAQVHTPLFSIEVESEEGIVAAPVADTAPAAVDH 207

Query: 61  ATASPVAAASRQRIPASPAVRRLVREHELNLSDIQGSGKDGRVLKADVLAYIEEGPKQAQ 120
                 A A   +  ASPAVRRL R ++++LS + GSGK GRV K DV  +     +  +
Sbjct: 208 EEVELHAPAGNGKALASPAVRRLARSYDIDLSLVPGSGKHGRVYKEDVERF--RSGEAVK 265

Query: 121 NQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAMAKSMVKSATTIPHFIYSEDIDV 180
            +A    AQ+  T +     A D   RVEPIRG+KA MAK M +S +TIPHF Y E++D+
Sbjct: 266 AKAAKAQAQSEPTAAPIAVSAGD---RVEPIRGVKAVMAKMMTESVSTIPHFTYCEELDL 322

Query: 181 TDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLNDDVTEIHYLPQCNI 240
           T+L+ LRE +K    +   +LT+MPFFMKAM+LA+ +FP +NS++NDD TE  +L   NI
Sbjct: 323 TELVALRESMKARYSSDDLKLTMMPFFMKAMSLALTQFPGINSRVNDDCTEQTFLASHNI 382

Query: 241 GMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQEDLKGGTITISNIGAL 300
           GMAVD K GL VPN+K V+  S+L +A E+ RLT+ ARSGRVS  DLKGG+I+ISNIGAL
Sbjct: 383 GMAVDSKVGLLVPNVKDVQQKSILEVAAEITRLTKDARSGRVSPADLKGGSISISNIGAL 442

Query: 301 GGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAGDHRIIDGGTIARFC 360
           GGT   PIIN PEVAIVALG+ Q LPRF+  G+V  R IM +SW+GDHR+IDGGTIARFC
Sbjct: 443 GGTVATPIINKPEVAIVALGKLQTLPRFNDKGEVEARKIMQISWSGDHRVIDGGTIARFC 502

Query: 361 NRWKGYLESPQTMLLHM 377
           N WK YLESPQ MLL M
Sbjct: 503 NLWKQYLESPQEMLLAM 519



 Score = 40.0 bits (92), Expect = 1e-07
 Identities = 27/89 (30%), Positives = 45/89 (50%), Gaps = 1/89 (1%)

Query: 1   MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60
           MTDKA+V+I A   G + KL++++  +A VH PL++ +  D E   +A T+      +  
Sbjct: 40  MTDKALVQIPAVHGGVIKKLHYKKGDIAIVHEPLYS-VEIDGELDGDATTESAAEEAVVQ 98

Query: 61  ATASPVAAASRQRIPASPAVRRLVREHEL 89
           + + PV    R      P +   + E EL
Sbjct: 99  SDSQPVVGGKRVEEFLLPDIGEGIVECEL 127


Lambda     K      H
   0.316    0.131    0.367 

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: 505
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 378
Length of database: 520
Length adjustment: 32
Effective length of query: 346
Effective length of database: 488
Effective search space:   168848
Effective search space used:   168848
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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