GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araZsh in Herbaspirillum seropedicae SmR1

Align Inner-membrane translocator (characterized, see rationale)
to candidate HSERO_RS05185 HSERO_RS05185 ABC transporter permease

Query= uniprot:A0KWY7
         (320 letters)



>FitnessBrowser__HerbieS:HSERO_RS05185
          Length = 340

 Score =  326 bits (835), Expect = 6e-94
 Identities = 168/305 (55%), Positives = 222/305 (72%), Gaps = 5/305 (1%)

Query: 11  ITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVI 70
           +T  LL+ M + G   +DGF S +V+ NLL DNAFLL+ A+GMT VI+SGGIDLSVG+V+
Sbjct: 20  VTVVLLVVMLVAGALGYDGFLSPQVMLNLLIDNAFLLVVAIGMTFVILSGGIDLSVGSVL 79

Query: 71  ALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARG 130
           AL+ +V + L+  + WHPLL  V +L +G  FGA MG +IH +KLQ FIVTLAGMFLARG
Sbjct: 80  ALTTMVAAFLLQNWHWHPLLVIVTVLLMGAGFGAAMGAMIHYFKLQAFIVTLAGMFLARG 139

Query: 131 LATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLS-SLIFILFFVIIAVVM-HYTRFGT 188
           L   +S  SI ID P +  +++  + L G   L +S S++  LF + +A+ M H TRFG 
Sbjct: 140 LCYLISINSITIDDPLFTTLSQTRLELAG---LFISPSVVIALFMLALAIWMAHCTRFGR 196

Query: 189 NVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDA 248
            VYAIGGN++SA LMG+ + +T + +YA S   A +AG++F+FY  SGY L A GVELDA
Sbjct: 197 AVYAIGGNENSALLMGLPVGRTKVLVYAFSGLCAAVAGVLFSFYMLSGYGLHAQGVELDA 256

Query: 249 IAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILL 308
           IAAVVIGGTLLTGG G+V GT+ GV+++GVIQT I FDG+LSSWWTKI IG LLF F + 
Sbjct: 257 IAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKIFIGALLFVFCVA 316

Query: 309 QKLLN 313
           Q++++
Sbjct: 317 QRVIS 321


Lambda     K      H
   0.330    0.145    0.424 

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: 408
Number of extensions: 16
Number of successful extensions: 2
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: 320
Length of database: 340
Length adjustment: 28
Effective length of query: 292
Effective length of database: 312
Effective search space:    91104
Effective search space used:    91104
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 (21.8 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