GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Azospirillum brasilense Sp245

Align Histidine transport system permease protein HisM (characterized)
to candidate AZOBR_RS00680 AZOBR_RS00680 ABC transporter permease

Query= SwissProt::P0A2I7
         (235 letters)



>FitnessBrowser__azobra:AZOBR_RS00680
          Length = 234

 Score =  115 bits (288), Expect = 7e-31
 Identities = 78/217 (35%), Positives = 120/217 (55%), Gaps = 12/217 (5%)

Query: 17  GYRFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTP-LYVQL 75
           G    G A+T+ + +S+ V+G +   + A  ++S N  +     ++T + RG P L V  
Sbjct: 14  GQLLGGAAMTVAVSVSAFVLGLVFGSLGASAKLSRNLALTGVAEVYTTVVRGVPELLVIY 73

Query: 76  LVFYSGMYTLEIV------KGTDLLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVP 129
           L+F+ G   +  V      +G   LNAF     +  VLA+ L + AY+TE+  GA+++VP
Sbjct: 74  LLFFGGSGAVMAVGRVFGYEGYIELNAF-----SIGVLAVGLISGAYSTEVIRGAVQAVP 128

Query: 130 HGEIEAARAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIA 189
           HG+IEAARA G S + + R I++P  LR ALP   N   L L  TAL     + ++++++
Sbjct: 129 HGQIEAARACGMSRWLILRRILVPQTLRYALPGLGNVWQLTLKDTALISVTALAEIMRVS 188

Query: 190 RDINSATYQPFTAFGIAAVLYLLISYVLISLFRRAER 226
                +T QPF  +  AAVLYLL++ V    F RAER
Sbjct: 189 HVAAGSTRQPFLFYTTAAVLYLLLTTVSTVAFERAER 225


Lambda     K      H
   0.330    0.141    0.429 

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: 145
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: 235
Length of database: 234
Length adjustment: 23
Effective length of query: 212
Effective length of database: 211
Effective search space:    44732
Effective search space used:    44732
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 (21.9 bits)
S2: 46 (22.3 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