GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Pantoea rwandensis LMG 26275

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_084938181.1 HA51_RS25215 ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>NCBI__GCF_002095475.1:WP_084938181.1
          Length = 355

 Score =  224 bits (572), Expect = 2e-63
 Identities = 133/327 (40%), Positives = 192/327 (58%), Gaps = 28/327 (8%)

Query: 36  KLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGT 95
           K   F +LL+++ FFSF  PNF+   NL+ + Q  A+ G+LAI  T VI+T GIDLSVG 
Sbjct: 13  KARTFIALLIVVGFFSFMVPNFLTTSNLLIMTQHVAITGLLAIGMTLVILTGGIDLSVGA 72

Query: 96  MMTFCAVMAGVVLTNWGMPL----------PLGIAAAIFFGALSGWISGMVIAKLKVPPF 145
           +   C ++AG +LTN G+PL          P  I     FG + G+I+G V+ +L V PF
Sbjct: 73  VAGICGMVAGALLTN-GVPLWGGNTLFFNVPEVILVVALFGIVLGFINGAVVTRLGVAPF 131

Query: 146 IATLGMMMLLKGLSLVISGTRPIYFN-------DTEGFSAIAQDSLIGDLIPS-LPIPNA 197
           I TLGMM + +G +L+ +     Y N          GF+ +   SL+G  IP  L +   
Sbjct: 132 ICTLGMMYVARGAALLFNDGST-YANLVGMPALGNTGFAFLGSGSLLGVYIPIWLMVGFL 190

Query: 198 VLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAG 257
           +L L+L          KT  GRY +A G NE A RL+GV +   KV VY FSG    + G
Sbjct: 191 LLGLYLT--------RKTPLGRYIYATGGNESAARLAGVPIIKVKVFVYAFSGLCAALVG 242

Query: 258 LIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIM 317
           LI+AS+L +A P  G  +E+DAI A V+GGT+L+GG G + G+IIGAF++  L +G+ +M
Sbjct: 243 LIVASQLQTAHPMTGNMFEMDAIGATVLGGTALAGGRGRVSGSIIGAFVIVFLADGMVMM 302

Query: 318 SVAQEWQTVVTGVIIILAVYLDILRRR 344
            V+  WQ V+ G++I+ AV +D  +++
Sbjct: 303 GVSDFWQMVIKGLVIVTAVVIDQFQQK 329


Lambda     K      H
   0.326    0.139    0.398 

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: 262
Number of extensions: 15
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: 347
Length of database: 355
Length adjustment: 29
Effective length of query: 318
Effective length of database: 326
Effective search space:   103668
Effective search space used:   103668
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 (21.7 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