GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21219 in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate HSERO_RS16730 HSERO_RS16730 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21219
         (281 letters)



>FitnessBrowser__HerbieS:HSERO_RS16730
          Length = 293

 Score =  141 bits (355), Expect = 2e-38
 Identities = 94/282 (33%), Positives = 147/282 (52%), Gaps = 11/282 (3%)

Query: 3   RQSPLFSVFIHASALLLAVVILAPVAWLLIMSISPAADL-SAKPLAWWPSDIDLSRYRTL 61
           + +P   V I+   L+   V+L P  W++I +  P  +L S     +W     L+ ++ L
Sbjct: 18  QSTPRKWVTIYIPLLIFLFVLLFPFYWMVITAFKPDNELLSQSGNPFWVIAPTLAHFKKL 77

Query: 62  LSAVENSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWSLYA--VIATY 119
           L   +      + A LLN++ V+ ++T A++  +V AA+A+ R            +   Y
Sbjct: 78  LFDTQ------YPAWLLNTVIVSVVSTFASLAASVFAAYAIERLRFQGSKQVGLGIFLAY 131

Query: 120 MLPPVALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMI 179
           ++PP  L +PL   +   GL ++ + L L Y T L PF TWLL   F SIP E+E  A+I
Sbjct: 132 LIPPSILFIPLAAIVFKLGLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALI 191

Query: 180 DGARLDQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAI-ADLA 238
           DGA   +IL  + LPLA P + ++ +FAF L+W+EF YAL F S    KT+ V I  +L 
Sbjct: 192 DGATRWEILVKIILPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELV 251

Query: 239 GGRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVK 280
            G V  +G +    +L +LP  ++        +SG+T G VK
Sbjct: 252 EGDVYHWGALMAGALLGSLPVAVVYSFFVEYYVSGMT-GAVK 292


Lambda     K      H
   0.325    0.136    0.402 

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: 204
Number of extensions: 10
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: 281
Length of database: 293
Length adjustment: 26
Effective length of query: 255
Effective length of database: 267
Effective search space:    68085
Effective search space used:    68085
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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