GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araH in Herbaspirillum seropedicae SmR1

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease

Query= CharProtDB::CH_014278
         (328 letters)



>FitnessBrowser__HerbieS:HSERO_RS03645
          Length = 339

 Score =  192 bits (487), Expect = 1e-53
 Identities = 111/303 (36%), Positives = 177/303 (58%), Gaps = 7/303 (2%)

Query: 27  MLVVFAVLFIACAIFVP-----NFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSV 81
           +LVV  +LF    +++      NFA+  N   +   ++++ ++A GM F + +   DLSV
Sbjct: 32  VLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSV 91

Query: 82  ASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQI 141
            SV+A + V   + ++L  +    +   +  G++ G+VNG ++A L INA + TL TM  
Sbjct: 92  GSVLAVSAVL-GMQVSLGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTA 150

Query: 142 VRGLAYIISDGKAVGIED-ESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNT 200
            RG AY+++DG  V   D  SF  +G  ++  +P  IW+ VA +++  ++L KT  G + 
Sbjct: 151 FRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHI 210

Query: 201 LAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVIS 260
            AIGGN +AARL G+ V    + ++ +SGL S +AG + ASR+         GYEL  I+
Sbjct: 211 YAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIA 270

Query: 261 ACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRY 320
           A VLGG SL GG+G I   V G LI+G + N + +L +S F QYV +G +++ AVI D++
Sbjct: 271 AVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKW 330

Query: 321 KQK 323
           +QK
Sbjct: 331 RQK 333


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: 300
Number of extensions: 17
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: 339
Length adjustment: 28
Effective length of query: 300
Effective length of database: 311
Effective search space:    93300
Effective search space used:    93300
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