GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Klebsiella michiganensis M5al

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate BWI76_RS07650 BWI76_RS07650 ABC transporter permease

Query= CharProtDB::CH_014278
         (328 letters)



>FitnessBrowser__Koxy:BWI76_RS07650
          Length = 351

 Score =  195 bits (495), Expect = 2e-54
 Identities = 112/318 (35%), Positives = 173/318 (54%), Gaps = 20/318 (6%)

Query: 31  FAVLFIACAIF---VPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIAC 87
           F  L +  A F   VPNF T  N+  +   ++++G++A GM   + +G  DLSV +V   
Sbjct: 17  FIALLLVIAFFSVMVPNFLTTSNLLIMTQHVAITGLLAIGMTLVILTGGIDLSVGAVAGI 76

Query: 88  AGVTTAVVINLTESLWIG----------VAAGLLLGVLCGLVNGFVIAKLKINALITTLA 137
            G+    ++     LW G          +    L GVL G VNG VI +  +   I TL 
Sbjct: 77  CGMVAGALLTNGLPLWNGSVIFFNVPEVILCVALFGVLVGFVNGAVITRFGVAPFICTLG 136

Query: 138 TMQIVRGLAYIISDGKAV----GIE---DESFFALGYANWFGLPAPIWLTVACLIIFGLL 190
            M + RG A + +DG       G+E   +  F  LG     G+  PIWL +  L++   L
Sbjct: 137 MMYVARGSALLFNDGSTYPNLNGMEALGNTGFSTLGSGTLMGIYLPIWLMIGFLLLGYWL 196

Query: 191 LNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMT 250
             KT  GR   AIGGNE AARLAGVP+V+ KI ++  SGL SA  G+I+AS++ +  PMT
Sbjct: 197 TTKTPLGRYIYAIGGNESAARLAGVPIVKAKIFVYAFSGLCSAFVGLIVASQLQTAHPMT 256

Query: 251 SIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLI 310
              +E+  I A VLGG +L GG G+++  + G  ++  + + M ++ +S F Q V++G++
Sbjct: 257 GNMFEMDAIGATVLGGTALAGGRGRVTGSIIGAFVIVFLADGMVMMGVSDFWQMVIKGVV 316

Query: 311 LLAAVIFDRYKQKAKRTV 328
           ++ AV+ D+++QK +  V
Sbjct: 317 IVTAVVVDQFQQKLQNKV 334


Lambda     K      H
   0.327    0.141    0.414 

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: 327
Number of extensions: 22
Number of successful extensions: 3
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: 328
Length of database: 351
Length adjustment: 28
Effective length of query: 300
Effective length of database: 323
Effective search space:    96900
Effective search space used:    96900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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