GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Pantoea rwandensis LMG 26275

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_084931811.1 HA51_RS03115 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A165ZSX8
         (514 letters)



>NCBI__GCF_002095475.1:WP_084931811.1
          Length = 504

 Score =  381 bits (978), Expect = e-110
 Identities = 206/501 (41%), Positives = 314/501 (62%), Gaps = 6/501 (1%)

Query: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75
           +    I K+F G+ AL         G+VHAL+GENGAGKSTL+++LGG + P SG +   
Sbjct: 6   IELRDIVKTFGGIHALKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPDSGTVYDK 65

Query: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTL 135
            + +  KG   ++A G+ +IHQE+ L  E+TVAEN+FL  LP     +    LR +A  +
Sbjct: 66  GEAVQIKGPKAAMARGITLIHQEMALAQELTVAENIFLHDLPT---FIAWPKLRAKAANI 122

Query: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195
           L+ L  EIDP   VG LS+  +Q+VEIA+ALS+ A VI FDEPT+ LS ++ +RL+ II 
Sbjct: 123 LRRLGFEIDPAATVGDLSVAHQQIVEIARALSQDARVIVFDEPTAVLSTQDANRLLEIIS 182

Query: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQD 255
            LR  G  ++Y+SHR++EVFRI + +T+ KDG+++ T E+  + T  +++  MVGR +  
Sbjct: 183 DLRSVGVAIVYISHRLDEVFRIADRMTIMKDGQWIAT-ESPQQTTLQEVIRLMVGRPVDQ 241

Query: 256 IYDYRPRE-RGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314
           ++  R     G+  L+V+ L        VSF V  GE++GL GLVG+GRTE+ RL+ G +
Sbjct: 242 LFSDRATYGMGEEVLRVEKLNARRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIFGAD 301

Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374
           R   G + LH K++ LRSP+ A+ AG+ L PEDRK++G++    +  N+ ++   +    
Sbjct: 302 RCDSGDIYLHGKKVSLRSPQQAVKAGIALVPEDRKRQGVVLDMPIRANVTMANDKAVMAP 361

Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434
              +    E     K  + +++K       +  LSGGNQQK +L +W ++  +V++LDEP
Sbjct: 362 LGFIHSSRETQVVSKLAQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNLGGQVIILDEP 421

Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494
           TRG+D+GAK EIYQ+I  LA  G+AV+V+SS+ +E+ G+ +R+LV+ EGA+ GEL  D  
Sbjct: 422 TRGVDVGAKREIYQLIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGAICGELQPDDY 481

Query: 495 NESNLLQLALP-RQRVADAAN 514
           +E NLL +A+  R  ++ A N
Sbjct: 482 SEENLLSMAMTHRSSLSHAEN 502


Lambda     K      H
   0.320    0.138    0.391 

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: 644
Number of extensions: 30
Number of successful extensions: 8
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: 514
Length of database: 504
Length adjustment: 34
Effective length of query: 480
Effective length of database: 470
Effective search space:   225600
Effective search space used:   225600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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