Alignments for a candidate for rbsA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Dinoroseobacter shibae DFL-12

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Dino:3609459
          Length = 548

 Score =  293 bits (749), Expect = 1e-83
 Identities = 184/502 (36%), Positives = 290/502 (57%), Gaps = 29/502 (5%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           ++L+GI KAF  V+A    ++ V PG +  ++GENGAGKST+M +L G Y  DAG +   
Sbjct: 26  IELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIK 85

Query: 65  GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124
           G++T     +++  AGIG++ Q   L+   T+ EN+ LG E     G +  +   A+A K
Sbjct: 86  GQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEE----GAL-LRPSLAKARK 140

Query: 125 LLAKLN----LRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180
           LL +L+    L    D L+ DLS+G QQ VEI K L  ++ ++I+DEPT  LT  E + L
Sbjct: 141 LLRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHL 200

Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240
           FR++  LK++G+ I+ I+H+++EI E  D V+V R G+  A  + A  + + L E+MVGR
Sbjct: 201 FRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVGR 260

Query: 241 KL---EDQYPHLDKAP----GDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTE 293
           K+    D+ P    AP     D+R+ VD+     V  +S  +R GE+LG++G+ G G++E
Sbjct: 261 KVLLRVDKTPAQPGAPILTVDDLRV-VDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSE 319

Query: 294 LMKVLYGALPRTSGYVTLDGHEV-VTRSPQDG---LANGIVYISEDRKRDGLVLGMSVKE 349
           L++VL G  P T G VT+ G ++ +T    +G    A GI ++ EDR+ +GL++     E
Sbjct: 320 LLEVLGGMRPAT-GRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYHAWE 378

Query: 350 NMSLTALRYFSRAGGSLKHADEQQAV----SDFIRLFNVKTPSMEQAIGLLSGGNQQKVA 405
           N+   A  Y      +     + +AV       I  F+V+      A    SGGNQQK+ 
Sbjct: 379 NV---AFGYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIV 435

Query: 406 IARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRI 465
           +AR +   P++L++ +PTRGVD+GA + I+Q I   +  G +I+LVS E+ E+L +SDR+
Sbjct: 436 LAREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRV 495

Query: 466 IVMHEGHLSGEFTREQATQEVL 487
            VM +G + GE    +  ++ L
Sbjct: 496 AVMFDGRIMGERPAAETNEKEL 517



 Score = 84.3 bits (207), Expect = 1e-20
 Identities = 63/225 (28%), Positives = 108/225 (48%), Gaps = 7/225 (3%)

Query: 270 DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGI 329
           D+S  +  G I G+ G  GAG++ LM +LYG     +G + + G +      Q  +  GI
Sbjct: 43  DISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIKGQKTEIPDSQAAIRAGI 102

Query: 330 VYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSM 389
             + +  K   LV   +V EN+ L A           K     + +S+   L NV   ++
Sbjct: 103 GMVFQHFK---LVENFTVLENVVLGAEEGALLRPSLAKARKLLRELSEEYEL-NVAPDAL 158

Query: 390 EQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSII 449
              I  LS G+QQ+V I + L  +  +LILDEPT  +       +++++   KA+G +II
Sbjct: 159 ---IEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLFRILEGLKAEGKTII 215

Query: 450 LVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           L++ ++ E++  +D + VM  G ++        + E L    VG+
Sbjct: 216 LITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVGR 260



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 63/235 (26%), Positives = 113/235 (48%), Gaps = 12/235 (5%)

Query: 16  GVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPKS 75
           GV+ + G +L V  G V+ + G  G G+S +++VL G+     G +   G++   TG  S
Sbjct: 290 GVERVKGISLQVRAGEVLGIAGVAGNGQSELLEVLGGMRPA-TGRVTVSGQQIDLTGKHS 348

Query: 76  SQEA--GIGIIH-----QELNLIPQLTIAENIFLGRE---FVNRFGKIDWKTMYAEADKL 125
           + +     GI H     Q   LI      EN+  G       NR   +D + + A+A+  
Sbjct: 349 NGKTRRAQGIAHVPEDRQAEGLIMDYHAWENVAFGYHDDPAYNRGLLMDNRAVRADAEGK 408

Query: 126 LAKLNLRFKSDKLVG-DLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVI 184
           +A+ ++R     L   + S G+QQ + +A+ +    +++++ +PT  +     E + + I
Sbjct: 409 IARFDVRPADCWLAAKNFSGGNQQKIVLAREIERNPELLLVGQPTRGVDIGAIEFIHQQI 468

Query: 185 RELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVG 239
             L+  G+ I+ +S  ++EI  + D V V  DG+ + ER  A   E  L  +M G
Sbjct: 469 IALRDAGKAILLVSVELEEILSLSDRVAVMFDGRIMGERPAAETNEKELGLLMAG 523


Lambda     K      H
   0.318    0.137    0.380 

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: 670
Number of extensions: 42
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 501
Length of database: 548
Length adjustment: 35
Effective length of query: 466
Effective length of database: 513
Effective search space:   239058
Effective search space used:   239058
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: 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources