Alignments for a candidate for HSERO_RS05250 in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Sinorhizobium meliloti 1021

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate SM_b20855 SM_b20855 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Smeli:SM_b20855
          Length = 504

 Score =  422 bits (1086), Expect = e-122
 Identities = 226/491 (46%), Positives = 324/491 (65%), Gaps = 12/491 (2%)

Query: 25  LRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGK 84
           L+++ K F G+ AL +  F++  GEVHAL+GENGAGKSTLM++L G      G+++++GK
Sbjct: 8   LKSISKSFGGIHALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQGEVVINGK 67

Query: 85  PVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAI 144
             E+ +PR A+ALGI +IHQEL L   LS A+NIF+G  P       I    L R+A  +
Sbjct: 68  RTELRDPRDARALGIVVIHQELALAPDLSVAENIFLGELPT-----LISRFSLRRRAKQL 122

Query: 145 FARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIR 204
             R+  D+DP   VG L+VA QQ+VEIAKALS D ++++ DEPTA L   +  +L +IIR
Sbjct: 123 IDRLGFDIDPGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLHQIIR 182

Query: 205 DLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGE 264
            L+ +GVGIVYISH++DE+  IADR++VM+DG+ + TV   +  +D II MMVGR +   
Sbjct: 183 GLRDRGVGIVYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKIDDIIRMMVGRPI--- 239

Query: 265 QRIPPDTSRNDV---VLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321
             + P+ S+  +   +L V+ LN GR +RDVSF++R GEI+G  GL+G+GRTEVARAIFG
Sbjct: 240 ANMFPERSQRTIGAELLNVKKLNAGRMVRDVSFSVRAGEIVGLGGLIGSGRTEVARAIFG 299

Query: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFT 381
           ADPL++G I + G    +KSP DAV  GIG + EDRK  G+ +   ++ N  ++ M    
Sbjct: 300 ADPLDSGTISLKGKALKLKSPRDAVKAGIGLVPEDRKEHGVVIDKPIRVNATMARMSSVV 359

Query: 382 R-VGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440
             +GF+     R       + L +K  S++     LSGGNQQK+V+AKW     D++  D
Sbjct: 360 NALGFLKPALERTDVTALGKSLRLKASSIDAPVSSLSGGNQQKVVLAKWFHAGGDVIILD 419

Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500
           EPTRG+DVGAK+EIY L++ LAE GKA+++ISSE  E+  +  RVL M +G+I GEL  +
Sbjct: 420 EPTRGVDVGAKAEIYALINKLAEDGKAVLVISSEHQELFGLCDRVLAMGQGQIRGELTPS 479

Query: 501 DATQEKIMQLA 511
           + ++E ++ L+
Sbjct: 480 NYSEENLLGLS 490



 Score = 94.7 bits (234), Expect = 7e-24
 Identities = 66/230 (28%), Positives = 115/230 (50%), Gaps = 9/230 (3%)

Query: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347
           A+R V+F +R GE+    G  GAG++ + R + G      GE++I+G +  ++ P DA A
Sbjct: 20  ALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQGEVVINGKRTELRDPRDARA 79

Query: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTP 407
            GI  + ++     LA  + V  NI L  +        + + ++R  A+  + +L     
Sbjct: 80  LGIVVIHQE---LALAPDLSVAENIFLGELPTL-----ISRFSLRRRAKQLIDRLGFDID 131

Query: 408 SVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKA 467
              +    LS  +QQ + IAK L +D  I+ FDEPT  +      ++++++  L ++G  
Sbjct: 132 P-GRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLHQIIRGLRDRGVG 190

Query: 468 IVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRESA 517
           IV IS  L EV  ++ R+ VM +G   G +A  D   + I+++   R  A
Sbjct: 191 IVYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKIDDIIRMMVGRPIA 240


Lambda     K      H
   0.320    0.135    0.372 

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: 709
Number of extensions: 34
Number of successful extensions: 8
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: 520
Length of database: 504
Length adjustment: 35
Effective length of query: 485
Effective length of database: 469
Effective search space:   227465
Effective search space used:   227465
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