GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Lactobacillus silagei IWT126

Align Putative ABC transporter arginine-binding protein 2 (characterized)
to candidate WP_089136315.1 CES79_RS03445 ABC transporter permease subunit

Query= SwissProt::P30859
         (243 letters)



>NCBI__GCF_002217945.1:WP_089136315.1
          Length = 479

 Score =  111 bits (278), Expect = 2e-29
 Identities = 71/239 (29%), Positives = 122/239 (51%), Gaps = 12/239 (5%)

Query: 5   LIAALIAGFSLSATAAE---TIRFATEASYPPFESIDANNQIVGFDVDLAQALCKEIDAT 61
           ++ A+   F L AT A+   T + AT++++PPFE  +++N+ VG D+DL  A+ K+    
Sbjct: 14  ILIAMFITFGLGATPAKATTTYQVATDSTFPPFEFANSHNKYVGIDIDLLHAIAKDQGFK 73

Query: 62  CTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQ-QGKYTS 120
                 +F+S + S++  + + V+AGM IT ERE    F+ PY+ +  +   +  GK T 
Sbjct: 74  VNIKPTSFNSAVQSVQSGQADGVIAGMSITKEREATFDFSKPYFMSGVVMAAKPNGKITK 133

Query: 121 VDQLKGKKVGVQNGTTHQKFIMDKHPE--ITTVPYDSYQNAKLDLQNGRIDGVFGDTAVV 178
           + QL+GK+V V+ GT+  ++    H +     V +D   +   D+  G     F D+ V+
Sbjct: 134 LSQLRGKRVAVKTGTSGAQYAQSIHKKYGFRIVTFDESNDMYQDVLTGNSAACFEDSPVM 193

Query: 179 TEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQG-NTELQQKLNTALEKVKKDGTYETI 236
              ++   KL     K+  K       G AV++G N +L +  N  L  +K +G Y  I
Sbjct: 194 KYAVRQGTKL-----KIYTKPTLNGPYGFAVKKGHNKKLLRMFNNGLADLKSNGEYARI 247


Lambda     K      H
   0.316    0.133    0.380 

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: 276
Number of extensions: 18
Number of successful extensions: 3
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: 243
Length of database: 479
Length adjustment: 28
Effective length of query: 215
Effective length of database: 451
Effective search space:    96965
Effective search space used:    96965
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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