Alignments for a candidate for HSERO_RS03640 in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Sinorhizobium meliloti 1021

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate SM_b20718 SM_b20718 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Smeli:SM_b20718
          Length = 508

 Score =  425 bits (1093), Expect = e-123
 Identities = 224/492 (45%), Positives = 316/492 (64%), Gaps = 4/492 (0%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           +L+ R I KSF     L  ++  +R GEIHALMGENGAGKSTL+K+LSG   P  GE+LL
Sbjct: 12  VLEARRISKSFSGVQVLFSVNFELRAGEIHALMGENGAGKSTLVKILSGFEQPSSGEVLL 71

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
           DG+PV L   GA+ A GI +I+QE  +A +++VA ++F+G E+ TR G++D   MR+ T 
Sbjct: 72  DGQPVTLPANGAAEALGIVIIHQEFNLAEHLTVAESLFLGREV-TRFGVLDRKYMRAETR 130

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            VL  LG    A+ L G LSIAE+Q VEIA+A+   +RIV MDEPTA LS  ET  LF  
Sbjct: 131 RVLDLLGCHVDANALIGSLSIAEKQMVEIAKAISRDARIVFMDEPTAVLSREETNFLFRQ 190

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           VR+LRD G + +++SH++ EV  L DRVTVLRDG +V       +D E I Q+MVGR +S
Sbjct: 191 VRKLRDRGTSFVFVSHKLDEVIELTDRVTVLRDGQWVKTAATSMLDGESIAQLMVGREMS 250

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLL 305
             +  ++    D      V++V A++   ++ A F+VR GE+LGF+G++G+GRTEL   +
Sbjct: 251 SLFPAKKEPNVDEE---VVLRVDAVSTDYVQDARFEVRKGEILGFSGMIGSGRTELMEAV 307

Query: 306 FGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASR 365
            G  PR  G++ + G  V      AA R G+AY+ +DRK +GL L   + AN T+    R
Sbjct: 308 AGLRPRLSGEVTIRGETVPSGDVHAANRRGLAYMTKDRKAKGLLLNSGMTANLTLQSLGR 367

Query: 366 HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLIL 425
           H R+G +   S     + A +R +++V        ++SGGNQQK+LLA+ +E  P ++I+
Sbjct: 368 HARIGYLSPASEAAALKRARRRFDIRVRDGNVVARRMSGGNQQKLLLAKVMETEPDIIII 427

Query: 426 DEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAG 485
           DEPTRG+D+  K +IY  +  LA  G +++V+SSE+PEVIG+C RV VMREG I G L G
Sbjct: 428 DEPTRGIDVGTKQQIYHFISALARDGRSIIVVSSEMPEVIGLCTRVAVMREGRIVGMLEG 487

Query: 486 AAITQENIMRLA 497
             I+++ IMR A
Sbjct: 488 DEISEQEIMRYA 499



 Score = 91.3 bits (225), Expect = 8e-23
 Identities = 61/230 (26%), Positives = 114/230 (49%), Gaps = 6/230 (2%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           +F++RAGE+    G  GAG++ L ++L G +  S G++LL+G+PV +    AA   GI  
Sbjct: 32  NFELRAGEIHALMGENGAGKSTLVKILSGFEQPSSGEVLLDGQPVTLPANGAAEALGIVI 91

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETP 398
           + ++       L   +    ++ +    TR G++  + +    R  +  L   V      
Sbjct: 92  IHQEFN-----LAEHLTVAESLFLGREVTRFGVLDRKYMRAETRRVLDLLGCHV-DANAL 145

Query: 399 VGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVIS 458
           +G LS   +Q V +A+ +    +++ +DEPT  +     + +++ V +L  +G + V +S
Sbjct: 146 IGSLSIAEKQMVEIAKAISRDARIVFMDEPTAVLSREETNFLFRQVRKLRDRGTSFVFVS 205

Query: 459 SELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPA 508
            +L EVI + DRV V+R+G      A + +  E+I +L     +    PA
Sbjct: 206 HKLDEVIELTDRVTVLRDGQWVKTAATSMLDGESIAQLMVGREMSSLFPA 255



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 62/225 (27%), Positives = 111/225 (49%), Gaps = 5/225 (2%)

Query: 22  LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAA 81
           + D    +R GEI    G  G+G++ LM+ ++G+     GE+ + G  V   D  A+   
Sbjct: 277 VQDARFEVRKGEILGFSGMIGSGRTELMEAVAGLRPRLSGEVTIRGETVPSGDVHAANRR 336

Query: 82  GINLIYQEL---AVAPNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGA 137
           G+  + ++     +  N  + AN+ + S  R  R+G +  A+  +      R+       
Sbjct: 337 GLAYMTKDRKAKGLLLNSGMTANLTLQSLGRHARIGYLSPASEAAALKRARRRFDIRVRD 396

Query: 138 SDL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAI 196
            ++ A R+S   QQ++ +A+ +     I+I+DEPT  +     +Q+++ +  L  +G +I
Sbjct: 397 GNVVARRMSGGNQQKLLLAKVMETEPDIIIIDEPTRGIDVGTKQQIYHFISALARDGRSI 456

Query: 197 IYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241
           I +S  M EV  L  RV V+R+G  VG L  DEI  + I++   G
Sbjct: 457 IVVSSEMPEVIGLCTRVAVMREGRIVGMLEGDEISEQEIMRYAAG 501


Lambda     K      H
   0.320    0.135    0.378 

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: 662
Number of extensions: 32
Number of successful extensions: 7
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: 521
Length of database: 508
Length adjustment: 35
Effective length of query: 486
Effective length of database: 473
Effective search space:   229878
Effective search space used:   229878
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:

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