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_b20855 SM_b20855 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Smeli:SM_b20855
          Length = 504

 Score =  421 bits (1083), Expect = e-122
 Identities = 227/495 (45%), Positives = 326/495 (65%), Gaps = 8/495 (1%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           T L  ++ I KSFG   AL  ++  +RPGE+HAL+GENGAGKSTLM+VL G   P QGE+
Sbjct: 3   TELANLKSISKSFGGIHALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQGEV 62

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
           +++G+   LRDP  +RA GI +I+QELA+AP++SVA N+F+G EL T   LI   ++R R
Sbjct: 63  VINGKRTELRDPRDARALGIVVIHQELALAPDLSVAENIFLG-ELPT---LISRFSLRRR 118

Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183
              ++ +LG       L G LS+A QQ VEIA+AL    +I++ DEPTA L  ++  +L 
Sbjct: 119 AKQLIDRLGFDIDPGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLH 178

Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243
            ++R LRD G+ I+YISHR+ EV+ +ADR+TV++DG  VG +   ++  + I++MMVGR 
Sbjct: 179 QIIRGLRDRGVGIVYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKIDDIIRMMVGRP 238

Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303
           ++  +  +R      A+L  V ++ A  G  +R  SF VRAGE++G  GL+G+GRTE+AR
Sbjct: 239 IANMFP-ERSQRTIGAELLNVKKLNA--GRMVRDVSFSVRAGEIVGLGGLIGSGRTEVAR 295

Query: 304 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM-NV 362
            +FGADP   G I L+G+ + +  PR A++AGI  VPEDRK  G+ +   +  NATM  +
Sbjct: 296 AIFGADPLDSGTISLKGKALKLKSPRDAVKAGIGLVPEDRKEHGVVIDKPIRVNATMARM 355

Query: 363 ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422
           +S    LG ++         A  + L +K +  + PV  LSGGNQQKV+LA+W      V
Sbjct: 356 SSVVNALGFLKPALERTDVTALGKSLRLKASSIDAPVSSLSGGNQQKVVLAKWFHAGGDV 415

Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482
           +ILDEPTRGVD+ AK+EIY L+++LA  G AV+VISSE  E+ G+CDRVL M +G I GE
Sbjct: 416 IILDEPTRGVDVGAKAEIYALINKLAEDGKAVLVISSEHQELFGLCDRVLAMGQGQIRGE 475

Query: 483 LAGAAITQENIMRLA 497
           L  +  ++EN++ L+
Sbjct: 476 LTPSNYSEENLLGLS 490



 Score =  100 bits (250), Expect = 1e-25
 Identities = 71/233 (30%), Positives = 115/233 (49%), Gaps = 9/233 (3%)

Query: 275 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRA 334
           +R  +FDVR GEV    G  GAG++ L R+L G    S G++++ G+   +  PR A   
Sbjct: 21  LRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQGEVVINGKRTELRDPRDARAL 80

Query: 335 GIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAH 394
           GI  + ++     L   ++VA N  +          L+   SL   A+  I RL   +  
Sbjct: 81  GIVVIHQEL---ALAPDLSVAENIFLGELPT-----LISRFSLRRRAKQLIDRLGFDI-D 131

Query: 395 PETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAV 454
           P   VG LS  +QQ V +A+ L    K+++ DEPT  +      +++Q++  L  +GV +
Sbjct: 132 PGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLHQIIRGLRDRGVGI 191

Query: 455 VVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAP 507
           V IS  L EV  I DR+ VM++G   G +A   +  ++I+R+     +    P
Sbjct: 192 VYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKIDDIIRMMVGRPIANMFP 244


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: 742
Number of extensions: 38
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: 521
Length of database: 504
Length adjustment: 35
Effective length of query: 486
Effective length of database: 469
Effective search space:   227934
Effective search space used:   227934
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