Alignments for a candidate for rbsA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Sinorhizobium meliloti 1021

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Smeli:SM_b20503
          Length = 512

 Score =  390 bits (1001), Expect = e-113
 Identities = 209/497 (42%), Positives = 309/497 (62%), Gaps = 9/497 (1%)

Query: 2   EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61
           E +L+++ + K F  VKAL+     +  G V AL GENGAGKST+M V+ G+     G +
Sbjct: 4   ETVLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEV 63

Query: 62  LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121
           L  G       P  +Q  GI ++HQE+ L P  TIAEN+F+      R   +++  +  +
Sbjct: 64  LIEGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQLERD 123

Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181
           A  ++ +L     S K VGDL I  QQ+VEIAK L+ + +V+I DEPT ALT+TE + LF
Sbjct: 124 AQAVMNRLAPIDVSQK-VGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQVLF 182

Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
            +IR+LK++G  I+YISHRM E+F +CD VTVFRDG+++A   V+ +T D ++ +MVGR+
Sbjct: 183 GIIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMVGRE 242

Query: 242 LEDQYPHLDKAP-----GDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMK 296
           +   YP  DK P     G+  L V +L G    DVSF LR GEILGV GL+G+GRTE+ +
Sbjct: 243 ISQLYP--DKQPSSERLGEPILSVRDLGGERFRDVSFELRYGEILGVGGLIGSGRTEIAE 300

Query: 297 VLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTAL 356
            +    P T G + L    +  R   D    G+VY+SEDRK  G+ L +S+ +N++   L
Sbjct: 301 GICALRPVTQGEIRLHDKVLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSIAQNIAALDL 360

Query: 357 RYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKV 416
           +  +   G L   +E+    D  R   V+   ++  +  LSGGNQQKVAIA+ L   PKV
Sbjct: 361 KALTSL-GLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIAKQLAVDPKV 419

Query: 417 LILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGE 476
           +++DEPTRG+DVGAK EI++L+ +    G+ I+++SSE+PE++G+ DR++V+ EG ++GE
Sbjct: 420 ILMDEPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLVVREGRIAGE 479

Query: 477 FTREQATQEVLMAAAVG 493
            +  + T+EV+M  A G
Sbjct: 480 VSGNEMTEEVIMRLASG 496



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 67/225 (29%), Positives = 107/225 (47%), Gaps = 9/225 (4%)

Query: 271 VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIV 330
           V F L +GE+  + G  GAG++ LM V+ G L  + G V ++G  V   SP    + GI 
Sbjct: 25  VDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEVLIEGAPVKIASPAVAQSLGIA 84

Query: 331 YISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHAD-EQQAVSDFIRLFNVKTPSM 389
            + ++     L    ++ ENM + A     R    + +A  E+ A +   RL  +    +
Sbjct: 85  LVHQEI---ALCPDATIAENMFMAATN--RRRSALMNYAQLERDAQAVMNRLAPI---DV 136

Query: 390 EQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSII 449
            Q +G L   +QQ V IA+ L    +VLI DEPT  +     + ++ +I   KA G+SII
Sbjct: 137 SQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQVLFGIIRDLKARGISII 196

Query: 450 LVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
            +S  M EV  + DR+ V  +G           T + ++   VG+
Sbjct: 197 YISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMVGR 241


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: 647
Number of extensions: 36
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 501
Length of database: 512
Length adjustment: 34
Effective length of query: 467
Effective length of database: 478
Effective search space:   223226
Effective search space used:   223226
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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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