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_b21376 SM_b21376 sugar uptake ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Smeli:SM_b21376
          Length = 503

 Score =  420 bits (1079), Expect = e-122
 Identities = 230/499 (46%), Positives = 333/499 (66%), Gaps = 12/499 (2%)

Query: 2   EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61
           + +L++  + K+F  V AL G  L V  GRV  L+GENGAGKST+MK+L G++   +G +
Sbjct: 7   DTILKITDVTKSFGQVAALKGMRLEVRRGRVHTLLGENGAGKSTLMKILAGVHGATSGEI 66

Query: 62  LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121
           +  G+      P+ +   G+ I+ QEL+L   LT+AENI   RE   RFG I+ K + A+
Sbjct: 67  VLDGQAYRPANPQEAASLGLAIVFQELSLCNNLTVAENILATRE-PRRFGFINDKALVAK 125

Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181
           A +++A L L     + VG+LSI  +Q+VEIAK LS ++KV+I+DEPT +L+D+E E LF
Sbjct: 126 AHRIVADLRLPIDVTEKVGNLSIAQRQLVEIAKGLSHDAKVVILDEPTSSLSDSEAEILF 185

Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
            +I  L+ +G  I+YISHRM+EI  + DD+TV RDG++++      +T ++LI +MVGR+
Sbjct: 186 EIIGRLRQRGAAIIYISHRMEEIMRLSDDITVIRDGEYVSTHARDEVTIETLIALMVGRR 245

Query: 242 LEDQYP----HL--DKAPGDIRLKVDNLCGPG-VNDVSFTLRKGEILGVSGLMGAGRTEL 294
           +++ YP    H+  D+AP    L VD L   G   DVSF +R GEILG  GL+G+GR+E+
Sbjct: 246 MDEIYPPPVHHVAADRAPV---LAVDRLTREGEFQDVSFDVRAGEILGFFGLVGSGRSEV 302

Query: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLT 354
           M  L+G +   +G V LDG  V  RSP   +A G+ +++E+RK +GLVLG SV+ N+S+ 
Sbjct: 303 MNALFG-MKSAAGTVRLDGEVVRFRSPDQAIARGVGFVTENRKEEGLVLGHSVEWNISMA 361

Query: 355 ALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP 414
           AL  F+   G +++  E+ A S+ +   ++KT S+E   G LSGGNQQK+ +A+ L+TRP
Sbjct: 362 ALADFAGGLGFIRNGAERAAASEQVGKLSIKTNSLETPAGALSGGNQQKIVLAKWLLTRP 421

Query: 415 KVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLS 474
           KVLILDEPTRGVDVGAK EIY++I +  A+G +I+L+SS++PEVLGMSDR++VMHEG   
Sbjct: 422 KVLILDEPTRGVDVGAKFEIYKIIRELAAEGTAILLISSDLPEVLGMSDRVVVMHEGAPG 481

Query: 475 GEFTREQATQEVLMAAAVG 493
                   T E +MA A G
Sbjct: 482 ATLEGSALTPETIMAHATG 500



 Score = 98.2 bits (243), Expect = 6e-25
 Identities = 67/221 (30%), Positives = 112/221 (50%), Gaps = 9/221 (4%)

Query: 275 LRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISE 334
           +R+G +  + G  GAG++ LMK+L G    TSG + LDG      +PQ+  + G+  + +
Sbjct: 32  VRRGRVHTLLGENGAGKSTLMKILAGVHGATSGEIVLDGQAYRPANPQEAASLGLAIVFQ 91

Query: 335 DRKRDGLVLGMSVKENMSLTAL-RYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAI 393
           +     L   ++V EN+  T   R F         A   + V+D     +V      + +
Sbjct: 92  ELS---LCNNLTVAENILATREPRRFGFINDKALVAKAHRIVADLRLPIDVT-----EKV 143

Query: 394 GLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSS 453
           G LS   +Q V IA+GL    KV+ILDEPT  +     + ++++I + +  G +II +S 
Sbjct: 144 GNLSIAQRQLVEIAKGLSHDAKVVILDEPTSSLSDSEAEILFEIIGRLRQRGAAIIYISH 203

Query: 454 EMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
            M E++ +SD I V+ +G       R++ T E L+A  VG+
Sbjct: 204 RMEEIMRLSDDITVIRDGEYVSTHARDEVTIETLIALMVGR 244


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: 643
Number of extensions: 41
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 501
Length of database: 503
Length adjustment: 34
Effective length of query: 467
Effective length of database: 469
Effective search space:   219023
Effective search space used:   219023
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