GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Shewanella amazonensis SB2B

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 6937555 Sama_1711 dihydrolipoamide acetyltransferase (RefSeq)

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



>FitnessBrowser__SB2B:6937555
          Length = 527

 Score =  388 bits (996), Expect = e-112
 Identities = 213/382 (55%), Positives = 267/382 (69%), Gaps = 12/382 (3%)

Query: 1   MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEP--EEARTKPEPAAQL 58
           MTDKA+V+I A KAG++  L++++  +AKVHAPL+A I  D E P    A      A Q 
Sbjct: 152 MTDKALVQIPALKAGKIVTLHYRKGQLAKVHAPLYA-IEVDAEHPVVPPAAAPAAAANQA 210

Query: 59  STATASPVAAASRQRIPASPAVRRLVREHELNLSDIQGSGKDGRVLKADVLAYIEEGPKQ 118
                S  A     +  ASPAVRR+ R  +++LS + GSGK GRV K D+  Y++ G   
Sbjct: 211 ERVAPSTAAVNGNGKALASPAVRRMARSLDVDLSLVPGSGKHGRVYKEDIEQYLKGGAAP 270

Query: 119 A---QNQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAMAKSMVKSATTIPHFIYS 175
           A   Q  AP    Q A T+SA   PAAD   RVEPIRG+KAAMA+ M+ S ++IPHF Y 
Sbjct: 271 APVAQTAAP----QAAVTQSAPVLPAADD--RVEPIRGVKAAMARQMMDSVSSIPHFTYC 324

Query: 176 EDIDVTDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLNDDVTEIHYL 235
           E+ID+T+L+ LRE++K +  +   +LT+MPFFMK+++LA+ EFPV+NSQ+N D TE+ Y 
Sbjct: 325 EEIDLTELVALRERMKAKYSSDDVKLTMMPFFMKSLSLALTEFPVVNSQVNADCTELTYK 384

Query: 236 PQCNIGMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQEDLKGGTITIS 295
              NIGMAVD K GL VPN+K V+S S+L +A E+ RLT+AARSGRVS  DLKGGTI+IS
Sbjct: 385 ASHNIGMAVDSKVGLLVPNVKDVQSKSILDVAREITRLTDAARSGRVSPADLKGGTISIS 444

Query: 296 NIGALGGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAGDHRIIDGGT 355
           NIGALGGT   PIIN PEVAIVALG+ Q LPRF A+G V  R IM VSW+GDHR+IDGGT
Sbjct: 445 NIGALGGTVATPIINKPEVAIVALGKLQTLPRFGADGSVQARKIMQVSWSGDHRVIDGGT 504

Query: 356 IARFCNRWKGYLESPQTMLLHM 377
           IARFCN WK YLE P+ MLL M
Sbjct: 505 IARFCNLWKQYLEQPEDMLLAM 526



 Score = 56.6 bits (135), Expect = 2e-12
 Identities = 34/75 (45%), Positives = 47/75 (62%), Gaps = 4/75 (5%)

Query: 1   MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQL-- 58
           MTDKA+V+I AP AG V+KLY+ +  +AKVHAPL+A +  + E  + +    E  AQ   
Sbjct: 40  MTDKALVQIPAPFAGVVSKLYYAKGEIAKVHAPLYA-VEMEGEGTDASAAPAEANAQAAH 98

Query: 59  -STATASPVAAASRQ 72
            S   A+PVA A +Q
Sbjct: 99  DSVPVAAPVAVAGKQ 113


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: 532
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: 527
Length adjustment: 32
Effective length of query: 346
Effective length of database: 495
Effective search space:   171270
Effective search space used:   171270
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.

Links

Downloads

Related tools

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