GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate AO356_21790 AO356_21790 sulfonate ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_21790
          Length = 282

 Score =  245 bits (626), Expect = 6e-70
 Identities = 125/234 (53%), Positives = 159/234 (67%)

Query: 19  QRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAE 78
           Q  +A+Q +D ++    FV +LGPSGCGKSTLL  +AG     SG + +DG  V GP  +
Sbjct: 25  QAFEAVQGLDCQIEAGQFVCVLGPSGCGKSTLLGALAGHLQPRSGSLNVDGLNVSGPSPQ 84

Query: 79  RGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSG 138
           RGMVFQ +TLFPW ++  N+ FGL+ RG+ +A++   A   +A VGL GF  H+P QLSG
Sbjct: 85  RGMVFQQHTLFPWRSVRDNVAFGLKMRGLGKAERHRAADEILALVGLEGFAGHWPDQLSG 144

Query: 139 GMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDE 198
           GMQQR  IAR L N P++LLMDEPFGALD  TR+ MQELLL IW   R TV+FVTHDIDE
Sbjct: 145 GMQQRVEIARVLVNRPRLLLMDEPFGALDALTRLNMQELLLDIWTRIRTTVVFVTHDIDE 204

Query: 199 AIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDLKARLTEEIRAE 252
           A+F+A+R+ V S RPGRI  +L +D P PR   + T PEF  LK    + +R E
Sbjct: 205 ALFLADRLLVMSPRPGRIIEDLRLDFPRPRTTELVTRPEFSRLKRHCLDLLRHE 258


Lambda     K      H
   0.322    0.136    0.394 

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: 239
Number of extensions: 5
Number of successful extensions: 1
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: 259
Length of database: 282
Length adjustment: 25
Effective length of query: 234
Effective length of database: 257
Effective search space:    60138
Effective search space used:    60138
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: 47 (22.7 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