GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2555 in Shewanella loihica PV-4

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate 5210738 Shew_3166 extracellular solute-binding protein (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_2555
         (249 letters)



>FitnessBrowser__PV4:5210738
          Length = 242

 Score =  119 bits (297), Expect = 7e-32
 Identities = 76/245 (31%), Positives = 127/245 (51%), Gaps = 12/245 (4%)

Query: 3   LRRNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFV---ENGKRTGFDIELVEAI 59
           + +++LLA   A    +   + QD ++ VGT+A FPP E+V      +  GFDI+L   +
Sbjct: 1   MNKSILLAGFTALLLLSGCGKEQDYLV-VGTNAAFPPFEYVGGVSGDQVMGFDIDLARKV 59

Query: 60  AKTMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVK 119
           A+  GK ++  ++ F  LI  L + + DM  S + IT ER+  VDF++ YY    VV+V 
Sbjct: 60  AEDAGKTLKVENMKFDSLIVALNAGKIDMIASGMTITPERQASVDFSEPYYEATQVVLVN 119

Query: 120 ADNKAINKLADLDGKKVSVQVGTKSVSYLTEKFPK---VQRVEVEKNQEMFNLVDIGRAD 176
             + +I+ LADL GK  +VQ+G+ +   + +K+ +         E   E+ N    G+ D
Sbjct: 120 KQDDSIHSLADLTGKHFAVQLGS-TADMMAKKYTQSVTAFNTGFEAIMELKN----GKVD 174

Query: 177 AAVTGKPAAFQYVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYA 236
             +     A  Y+   P L+++      E YG A+ K  PEL  ++N  +  +K +G Y 
Sbjct: 175 LVLFDSEPAANYLAKNPELKLISLDFPPEFYGFAVAKSQPELLASINKTLATMKQNGEYD 234

Query: 237 AIVKK 241
           A++ K
Sbjct: 235 ALLAK 239


Lambda     K      H
   0.317    0.133    0.369 

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: 141
Number of extensions: 5
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: 249
Length of database: 242
Length adjustment: 24
Effective length of query: 225
Effective length of database: 218
Effective search space:    49050
Effective search space used:    49050
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 (21.7 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