GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Pseudomonas fluorescens FW300-N2C3

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate AO356_28995 AO356_28995 ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28995
          Length = 258

 Score =  189 bits (481), Expect = 3e-53
 Identities = 104/244 (42%), Positives = 158/244 (64%), Gaps = 6/244 (2%)

Query: 2   TTNILKVQQLSVAY-GGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRV 60
           ++ +L VQ + V Y G I AV G+ L V +G++V L+GANGAGK+TTLKAI+G + A R 
Sbjct: 11  SSELLAVQDIEVIYDGAILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRA 70

Query: 61  E---GHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYT-SDDKGQI 116
           +   G I + GQ   G  +  L +  +  V EGR VF  ++I++NL  G +     + ++
Sbjct: 71  QVSRGRIVFQGQDTAGVAANLLARRGIVHVLEGRHVFAHLTIEDNLRSGGFLRKPTRREL 130

Query: 117 AADIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMV 176
             D+++ +A FPRLK +    AG  SGGEQQMLA+ RALM+ P+L+LLDEPSMGL+PI+V
Sbjct: 131 EHDLERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTQPRLVLLDEPSMGLAPILV 190

Query: 177 EKIFEVIRNVSAQ-GITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKA 235
           E+IF ++  ++AQ G++ L+ EQN  +AL  A   Y++E+G +  +G A ++     ++ 
Sbjct: 191 EEIFAIVAQLNAQEGVSFLVAEQNINVALRHASYAYILENGRVVGEGDATELAAREDLQH 250

Query: 236 AYLG 239
            YLG
Sbjct: 251 FYLG 254


Lambda     K      H
   0.317    0.134    0.365 

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: 154
Number of extensions: 7
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: 241
Length of database: 258
Length adjustment: 24
Effective length of query: 217
Effective length of database: 234
Effective search space:    50778
Effective search space used:    50778
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: 46 (22.3 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