GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Herbaspirillum seropedicae SmR1

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate HSERO_RS20055 HSERO_RS20055 metal-dependent hydrolase

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__HerbieS:HSERO_RS20055
          Length = 597

 Score =  199 bits (507), Expect = 1e-55
 Identities = 115/258 (44%), Positives = 158/258 (61%), Gaps = 8/258 (3%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           LL+V+ ++ +FGGL+A+ND SF+ K G+I  LIGPNGAGK+T FN +TG    + G + F
Sbjct: 345 LLEVDQINKRFGGLVAVNDVSFKVKAGEIVGLIGPNGAGKSTTFNLVTGLLHASGGRVGF 404

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
           N +      +  LP  R      +ARTFQ++RL  G+TVLEN+ +  H +  +      +
Sbjct: 405 NGRD-----IAGLP-ARAIARLGIARTFQHVRLLPGMTVLENVALGAHMRSQQGFLKNTV 458

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
             +       E A   E AR  L +  L     + AG+L  G QR LEIARA+C  P LL
Sbjct: 459 NAMLHLERAEEQALLDEAARA-LHRVGLQHLMHEQAGNLALGQQRILEIARALCCDPLLL 517

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEPAAGL   E   L+ +L+ +RA+ G SILL+EHDM  VME++DH+VV+E+G KI++
Sbjct: 518 LLDEPAAGLRHLEKQALSKVLQELRAD-GMSILLVEHDMEFVMELTDHIVVMEFGAKIAE 576

Query: 254 GTPDHVKNDPRVIAAYLG 271
           GTP  +   P VI AYLG
Sbjct: 577 GTPQEIARHPAVIEAYLG 594


Lambda     K      H
   0.318    0.136    0.386 

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: 418
Number of extensions: 23
Number of successful extensions: 4
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: 292
Length of database: 597
Length adjustment: 31
Effective length of query: 261
Effective length of database: 566
Effective search space:   147726
Effective search space used:   147726
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 (21.7 bits)
S2: 50 (23.9 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