GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16935 in Pseudomonas fluorescens GW456-L13

Align L-arabinose-binding periplasmic protein; Short=ABP (characterized, see rationale)
to candidate PfGW456L13_2120 L-arabinose-binding periplasmic protein precursor AraF (TC 3.A.1.2.2)

Query= uniprot:A0A161H4E4
         (334 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2120
          Length = 334

 Score =  593 bits (1530), Expect = e-174
 Identities = 295/334 (88%), Positives = 311/334 (93%)

Query: 1   MKHRRGIRSLCRAALAVTAVSLSSHLLAADAVKIGFLVKQAEEPWFQTEWAFAEKAAKDK 60
           M  R  IRSLC AALAV+A SLS+ LLAA+ VKIGFLVKQAEEPWFQTEWAFAEKA K+K
Sbjct: 1   MNRRHAIRSLCCAALAVSAFSLSNTLLAAEEVKIGFLVKQAEEPWFQTEWAFAEKAGKEK 60

Query: 61  GFQLIKIAVPDGEKTLSAIDSLAANGAKGFVICPPDVSLGPAIVAKAKLNDMKVIAVDDR 120
           GF LIKIAVPDGEKTLSAIDSLAANGAKGFVICPPDVSLGPAI+AKAKLN +KVIAVDDR
Sbjct: 61  GFTLIKIAVPDGEKTLSAIDSLAANGAKGFVICPPDVSLGPAIMAKAKLNGLKVIAVDDR 120

Query: 121 FVGSDGKFMEDVPYLGMAAFEVGQKQGGAMAAEAKKRGWDWKDTYAVINTYNELDTGKKR 180
           FV + GKFMEDVPYLGMAAFEVGQKQG AMA EAKKRGWDWKDTYAVINTYNELDTGKKR
Sbjct: 121 FVDASGKFMEDVPYLGMAAFEVGQKQGNAMATEAKKRGWDWKDTYAVINTYNELDTGKKR 180

Query: 181 TDGSVDALKKAGMPADHILYSALKTLDVPGSMDSTNSALVKLPSAAKNLIIGGMNDNTVL 240
           TDGSV AL+ AGMP DHIL++ALKTLDVPGSMD+TNSALVKLP AAKNLIIGGMNDNTVL
Sbjct: 181 TDGSVKALQDAGMPKDHILFAALKTLDVPGSMDATNSALVKLPGAAKNLIIGGMNDNTVL 240

Query: 241 GGVRATEAAGFKAANVIGIGINGTDAIGELKKPDSGFFGSMLPSPHIEGYKTAEMMYEWI 300
           GGVRATE+AGF AANVIGIGINGTDAIGELKKPDSGF+GSMLPSPHIEGY TA MMYEW+
Sbjct: 241 GGVRATESAGFAAANVIGIGINGTDAIGELKKPDSGFYGSMLPSPHIEGYNTASMMYEWV 300

Query: 301 TTGKEPPKYTAMDEVTLITRENFKQELEKIGLWN 334
           TTGKEP KYTAMD+VTLITR+NFKQELEKIGLWN
Sbjct: 301 TTGKEPAKYTAMDDVTLITRDNFKQELEKIGLWN 334


Lambda     K      H
   0.316    0.133    0.388 

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: 501
Number of extensions: 15
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: 334
Length of database: 334
Length adjustment: 28
Effective length of query: 306
Effective length of database: 306
Effective search space:    93636
Effective search space used:    93636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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