GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Pseudomonas fluorescens FW300-N2E3

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate AO353_20825 AO353_20825 ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20825
          Length = 325

 Score =  198 bits (503), Expect = 2e-55
 Identities = 121/307 (39%), Positives = 178/307 (57%), Gaps = 7/307 (2%)

Query: 33  LGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSI 92
           LG+   L+ +   FSVL+ +F  +   S +A Q    MVLA GMTFV++ GGIDLSVGS+
Sbjct: 21  LGLAGALLAMIALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSV 80

Query: 93  LSISAVVAMLVSLMPQLGMLSVPAALL---CGLLFGIVNGALVAFMKLPPFIVTLGTLTA 149
           L+++     +  L    G   +PAALL      + G + G++    ++P FIV+LG L  
Sbjct: 81  LALAGSTVSVAIL--GWGWSVLPAALLGMAAAAVAGTITGSITVAWRIPSFIVSLGVLEM 138

Query: 150 VRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIY 209
            RG+A  +    T Y  D  FA++ N    G+    IIA  V+ ++  VL RTV G  + 
Sbjct: 139 ARGVAYQMTGSRTAYIGD-AFAWLSNPITFGISPSFIIALLVIFIAQAVLTRTVFGRYLI 197

Query: 210 AVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIA 269
            +G N EA RL+GI      + V+++ GLLAG+  +   +RL AA+    G   EL  IA
Sbjct: 198 GIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADP-NAGSGLELQVIA 256

Query: 270 AVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSY 329
           AV++GGTS +GG GS++ T  G LII+VL+ GL  +G ++  + II G VI+ AV LD+Y
Sbjct: 257 AVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTY 316

Query: 330 RRKGSAR 336
           R + ++R
Sbjct: 317 RSQRASR 323


Lambda     K      H
   0.325    0.141    0.409 

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: 371
Number of extensions: 26
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: 337
Length of database: 325
Length adjustment: 28
Effective length of query: 309
Effective length of database: 297
Effective search space:    91773
Effective search space used:    91773
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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