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_RS14705 HSERO_RS14705 ABC transporter

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__HerbieS:HSERO_RS14705
          Length = 253

 Score =  194 bits (493), Expect = 2e-54
 Identities = 114/262 (43%), Positives = 160/262 (61%), Gaps = 12/262 (4%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           LL++  +S  FGGL  +   +F  ++G+I  LIGPNGAGKTTVFN ITG  + + G I F
Sbjct: 2   LLQLNDISKNFGGLQVLQGVNFNVRQGEIFGLIGPNGAGKTTVFNLITGLLRASSGSIRF 61

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
           N        +  +   +IT E  +ARTFQNIR+F  +T+LEN++V  H+ L       +L
Sbjct: 62  NDDD-----IGAVAPHKIT-ERGIARTFQNIRVFKEMTLLENVVVGMHDHLNYGVASMLL 115

Query: 134 GLIGVGPYKREAAE-AIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192
            L G    ++EA E A+EL    L    L  +A   A  L YG QR+LE ARA+ T P+L
Sbjct: 116 NLGGFRNAEKEARERALEL----LSWVRLDHKAHMLADSLSYGEQRKLEFARALATKPKL 171

Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252
           L LDEP AG+NP E   L + + +I+ + G +I +IEHDM  VM + + + VL +G+ I+
Sbjct: 172 LLLDEPVAGMNPAEKTELMSEIVNIK-QRGFTIFMIEHDMRFVMGLCERIAVLNFGKIIA 230

Query: 253 DGTPDHVKNDPRVIAAYLGVED 274
           +GTPD +KN+  VI AYLG E+
Sbjct: 231 EGTPDQIKNNQEVIEAYLGKEE 252


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: 198
Number of extensions: 11
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: 253
Length adjustment: 25
Effective length of query: 267
Effective length of database: 228
Effective search space:    60876
Effective search space used:    60876
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: 47 (22.7 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