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_084935382.1 HA51_RS14780 ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>NCBI__GCF_002095475.1:WP_084935382.1
          Length = 366

 Score =  228 bits (580), Expect = 2e-64
 Identities = 129/326 (39%), Positives = 203/326 (62%), Gaps = 25/326 (7%)

Query: 36  KLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGT 95
           KL  F +L L++ FF+   P+F+ V ++V +++  A+N  LA+  T+VIIT+GIDLS+G 
Sbjct: 28  KLRTFIALFLIVGFFAITVPDFLAVGSMVIMVKHIAINAFLALGITFVIITAGIDLSIGA 87

Query: 96  MMTFCAVMAGVVLTNWGMPLPL-GIAA----------AIFFGALSGWISGMVIAKLKVPP 144
            +  C ++AG ++T  G+ LP+ GIA            +  G L G  +G +I K  V P
Sbjct: 88  TLGLCGMVAGWLITK-GIVLPMFGIAIFPSVWVIVPLVLVVGGLIGAANGWIITKYNVAP 146

Query: 145 FIATLGMMMLLKGLSLVISG--TRPIYFNDTE----GFSAIAQDSLIGDLIPSLPIPNAV 198
           FI TLG M +L+G +++ SG  T P    + +    GF  I     +G       +P A+
Sbjct: 147 FICTLGTMYILRGTAMLTSGGETFPGLQGNPQLGNTGFDKIGAGYFLG-------LPWAI 199

Query: 199 LILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGL 258
            ++ ++A+  + +  +  FGR  +A+G NE A  LSGVKV   K+ VYT SG    IAG+
Sbjct: 200 WMMVVLALVIAYVARRLPFGRQVYAIGDNERAAELSGVKVKSVKIWVYTISGFCAAIAGI 259

Query: 259 IIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMS 318
           +++S+L ++ PA G  +E++AIAAVV+GGTSL+GG GTILGT++GAF++  L +GL +M 
Sbjct: 260 VVSSQLVASHPANGTSFEMNAIAAVVLGGTSLAGGRGTILGTLVGAFVIGFLADGLIMMG 319

Query: 319 VAQEWQTVVTGVIIILAVYLDILRRR 344
           V++ WQ V+ G++II+AV +D ++ R
Sbjct: 320 VSEFWQMVIKGIVIIVAVIIDQMQSR 345


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: 289
Number of extensions: 17
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: 366
Length adjustment: 29
Effective length of query: 318
Effective length of database: 337
Effective search space:   107166
Effective search space used:   107166
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.

Links

Downloads

Related tools

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