GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Klebsiella michiganensis M5al

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate BWI76_RS05870 BWI76_RS05870 ABC transporter

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



>FitnessBrowser__Koxy:BWI76_RS05870
          Length = 247

 Score =  199 bits (507), Expect = 3e-56
 Identities = 100/210 (47%), Positives = 137/210 (65%)

Query: 19  QRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAE 78
           Q+  ALQ    ++   + V ++G SGCGKSTLLR++ GL+ AT G + ++G PV G G E
Sbjct: 17  QQVTALQNFSLDIAAGELVALVGSSGCGKSTLLRMLVGLESATQGEIRINGEPVTGVGKE 76

Query: 79  RGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSG 138
           RG+VFQ   LFPWL +  N+  GL +  +  A +++RA   + +V L  F    P QLSG
Sbjct: 77  RGIVFQEPRLFPWLNVLDNVMLGLADEKLSRAAKRQRALEMLERVQLSEFANALPAQLSG 136

Query: 139 GMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDE 198
           GM QR AIAR L   P+IL++DEPFGALD  TR  +Q+ LL I +    T L VTHD++E
Sbjct: 137 GMAQRVAIARGLVARPQILMLDEPFGALDALTRHTLQQELLQIHQRAGTTTLLVTHDVEE 196

Query: 199 AIFMANRVAVFSARPGRIKTELAVDLPHPR 228
           A+ +A+RV V S RPGRI+  +++ LPHPR
Sbjct: 197 AVALADRVVVLSPRPGRIREVVSLALPHPR 226


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: 156
Number of extensions: 9
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: 247
Length adjustment: 24
Effective length of query: 235
Effective length of database: 223
Effective search space:    52405
Effective search space used:    52405
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: 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