GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Klebsiella michiganensis M5al

Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate BWI76_RS08105 BWI76_RS08105 glutamate/aspartate ABC transporter permease GltJ

Query= SwissProt::P0AER3
         (246 letters)



>FitnessBrowser__Koxy:BWI76_RS08105
          Length = 246

 Score =  456 bits (1172), Expect = e-133
 Identities = 221/246 (89%), Positives = 231/246 (93%)

Query: 1   MSIDWNWGIFLQQAPFGNTTYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNRF 60
           MSIDWNWGIFLQQAPFGNTTYLGW+WSGFQVT+ LS+ AWIIAF VGS FGILRTVPNR 
Sbjct: 1   MSIDWNWGIFLQQAPFGNTTYLGWLWSGFQVTVTLSVTAWIIAFFVGSLFGILRTVPNRL 60

Query: 61  LSGLGTLYVELFRNVPLIVQFFTWYLVIPELLPEKIGMWFKAELDPNIQFFLSSMLCLGL 120
           LS +GT YVELFRNVPLIVQFFTWYLV+PELLPE IGMWFK+ELDPNIQFF+SSMLCLGL
Sbjct: 61  LSTIGTCYVELFRNVPLIVQFFTWYLVVPELLPENIGMWFKSELDPNIQFFVSSMLCLGL 120

Query: 121 FTAARVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLV 180
           FTAARVCEQVR+ IQSLPRGQKNA LAMGLTLPQ YRYVLLPNAYRVIVPPMTSEMMNLV
Sbjct: 121 FTAARVCEQVRSGIQSLPRGQKNAGLAMGLTLPQTYRYVLLPNAYRVIVPPMTSEMMNLV 180

Query: 181 KNSAIASTIGLVDMAAQAGKLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVRLP 240
           KNSAIASTIGL DMAAQAGKLLDYSAHAWESFTAITLAYV INA IML+M +VERKVRLP
Sbjct: 181 KNSAIASTIGLADMAAQAGKLLDYSAHAWESFTAITLAYVFINAVIMLIMYVVERKVRLP 240

Query: 241 GNMGGK 246
           GNMGGK
Sbjct: 241 GNMGGK 246


Lambda     K      H
   0.328    0.140    0.443 

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: 349
Number of extensions: 6
Number of successful extensions: 1
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: 246
Length of database: 246
Length adjustment: 24
Effective length of query: 222
Effective length of database: 222
Effective search space:    49284
Effective search space used:    49284
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: 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