GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Dyella japonica UNC79MFTsu3.2

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

Query= uniprot:D8IUD1
         (522 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  324 bits (830), Expect = 5e-93
 Identities = 198/479 (41%), Positives = 282/479 (58%), Gaps = 11/479 (2%)

Query: 13  LLTLSGIGKRYAAPV-LDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMML 71
           +L   G+GKR+ A + LDG+DL LR G+V AL G+NGAGKSTL K++ G+     G + L
Sbjct: 12  VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71

Query: 72  DGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLP--RRFGWIDRKKLAEAA 129
           DG+  AP++  +A+  GI  V QE+NL P LS+AENL+  + P  RR   ID +++ + A
Sbjct: 72  DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGA 131

Query: 130 RAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLF 189
           R+ +  + L ELD   P+G   +  +QMV IAR L  S R LILDEPT+ L   EV  LF
Sbjct: 132 RSLLRQLHL-ELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190

Query: 190 SRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGEL 249
             I +LR  G+AI++++H L+++  ++DRI VLRDG  V    +       LV  M G  
Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRD 250

Query: 250 TKVDLDAEHRRI----GAPVLRIRGLGRAPVVHPASLALHAGEVLGIAGLIGSGRTELLR 305
                 A+  R       P +  +GLG    +HP  L +  GE+LG+ GL+GSGRTEL R
Sbjct: 251 LPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELAR 310

Query: 306 LIFGADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLA 365
           L+FG DRAE+GE+ IG   E   ++ P DAV  G+A+  E+RK  G++   ++  N  LA
Sbjct: 311 LLFGLDRAERGELRIGG--ERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLA 368

Query: 366 NLGSVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCP 425
                   GM   A +  +A+  V+ L I++  +    G LSGGNQQKV++ARWL  +  
Sbjct: 369 LQARQGWRGM-SRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPR 427

Query: 426 IMLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIA 484
           +++ DEPTRGID+ AK ++       A  G  +L +S++  EL + CDRIAVM   R A
Sbjct: 428 LLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKA 486


Lambda     K      H
   0.320    0.137    0.390 

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: 762
Number of extensions: 45
Number of successful extensions: 9
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: 522
Length of database: 505
Length adjustment: 35
Effective length of query: 487
Effective length of database: 470
Effective search space:   228890
Effective search space used:   228890
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 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