GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-C in Photobacterium gaetbulicola Gung47

Align Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate WP_044620926.1 H744_RS02965 PTS fructose transporter subunit IIC

Query= TCDB::Q5V5X5
         (383 letters)



>NCBI__GCF_000940995.1:WP_044620926.1
          Length = 373

 Score =  206 bits (524), Expect = 9e-58
 Identities = 118/355 (33%), Positives = 194/355 (54%), Gaps = 32/355 (9%)

Query: 20  TSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGW----------FLAQ 69
           T VK  +MTGVS+M+P +  G + + +A  IG +    +N                F A 
Sbjct: 15  TEVKTAIMTGVSYMLPLIIAGAVIMGIA-RIGASFYGIDNIWDGSHAEAANAVVRLFHAF 73

Query: 70  IGVAGL--TIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAG 127
            G  GL  ++M+P++ GYIA++IAD+PG+APG                  V G+   E G
Sbjct: 74  DGFGGLALSLMLPVVAGYIAFSIADKPGIAPGM-----------------VAGLLAKEMG 116

Query: 128 AGYLGAIVAGLLAGYVARFF-KNLDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVA 186
            G+LGA+ AG +AGY+ +     + +P+ +    P+ +IPV    +   +M++++G P+A
Sbjct: 117 TGFLGALAAGFIAGYIVKLLVTKVKLPKSVASAGPIFIIPVGGTLLACLVMMYIIGDPLA 176

Query: 187 LANEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAV 246
             N GL ++L  M  G  IV+  ++GGM+ FD+GGP+NK A   A  ++   IY P  A 
Sbjct: 177 AMNRGLENWLLGMSDGNKIVLAAVVGGMVGFDLGGPINKAAVTTAMAMLASGIYDPNTAA 236

Query: 247 MIGGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAI 306
            +  +IPPIG+ ++  I   ++   + + GK+  ++GL  ++EGAIP+A A+P ++I   
Sbjct: 237 QVAIIIPPIGIGVATLIWKQRFPHSLQDAGKASTLMGLIGVSEGAIPFALANP-KIIVVN 295

Query: 307 VAGSAVGGATSMALGVTMPAPHGGIFVVLLSNQPLAFLGSILLGSLVTAVVATVI 361
           V GSAVG A ++ LG    AP  G +  L     L ++ +I +GS + AV + ++
Sbjct: 296 VIGSAVGSALAVGLGAVNRAPISGFYGWLAVENWLVYVLAIAVGSGIIAVGSLLV 350


Lambda     K      H
   0.322    0.139    0.399 

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: 35
Number of successful extensions: 4
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: 383
Length of database: 373
Length adjustment: 30
Effective length of query: 353
Effective length of database: 343
Effective search space:   121079
Effective search space used:   121079
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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