GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate AO353_23185 AO353_23185 ABC transporter ATP-binding protein

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



>FitnessBrowser__pseudo3_N2E3:AO353_23185
          Length = 278

 Score =  191 bits (485), Expect = 1e-53
 Identities = 102/248 (41%), Positives = 153/248 (61%), Gaps = 2/248 (0%)

Query: 2   SSVSIQAVSRVFET-AKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHA 60
           + +  + V + F    K +   A++ V+F++R  + V+I+GPSGCGKST+L + +GL   
Sbjct: 20  TEIEFRNVGKCFPAKGKSEAPFAIREVNFKIRRGEVVSIIGPSGCGKSTILNMGSGLYRP 79

Query: 61  TSGRVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFI 120
           T G V + G  V GP  +   + Q   L PW +I +N+  GL  +G+P A+++  A   +
Sbjct: 80  TEGEVFVAGEAVTGPVRQVAFMLQKDLLMPWRSIRRNVELGLEIQGVPAAKRQAVAKDLL 139

Query: 121 AKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLG 180
            +  L+GF  H+P QLSGGM+QR A+AR LA DP++L +DEPF ALD QT++++Q+ +  
Sbjct: 140 DRCHLQGFADHYPFQLSGGMRQRAALARTLAIDPQVLFLDEPFSALDAQTKMILQQDMAR 199

Query: 181 IWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLP-HPRHYTIKTSPEFM 239
           +   E+KT LF+THD+ EAI M++R+ V SARPG I  E+ VDLP        +  PE  
Sbjct: 200 MLFDEKKTALFITHDLIEAIAMSDRLLVMSARPGTIIEEITVDLPFRDNPLERRKLPEIG 259

Query: 240 DLKARLTE 247
            L  RL E
Sbjct: 260 PLVGRLME 267


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: 183
Number of extensions: 7
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: 278
Length adjustment: 25
Effective length of query: 234
Effective length of database: 253
Effective search space:    59202
Effective search space used:    59202
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