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 SMc02337 SMc02337 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Smeli:SMc02337
          Length = 501

 Score =  414 bits (1064), Expect = e-120
 Identities = 224/497 (45%), Positives = 317/497 (63%), Gaps = 13/497 (2%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           T L+ + GI K+F    AL  +   +R GE+HAL+GENGAGKSTLM+VL+G   P  G +
Sbjct: 2   TVLVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTV 61

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
            + G  +    P  +   GI++I+QELA+AP+++VA N+F+G   R    +++H  +R  
Sbjct: 62  SIHGETMQHSGPRGAAGRGISVIHQELALAPDLTVAENIFLGRLPR----IVNHRRLRKA 117

Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183
              +L +LG     +  AGRL++A QQ VEIA+AL +R+RI++ DEPTA L+  + E+L 
Sbjct: 118 ASEILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERLL 177

Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243
            ++R LR  G   +YISHR+ EV+ L+DR+TV++DGS V  L     D + ++  MVGR 
Sbjct: 178 AIIRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMVGRQ 237

Query: 244 LSEFYQHQRIAPADAAQLP--TVMQVRALAGG-KIRPASFDVRAGEVLGFAGLVGAGRTE 300
           +S  +      P+ A ++P   V++VR ++ G K+R  SF VRAGEV+G  GLVG+GRTE
Sbjct: 238 MSALF------PSKAGRVPGEVVVRVRNVSRGRKVRDVSFSVRAGEVVGLGGLVGSGRTE 291

Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360
           +ARL+FGAD    G + L G+P+H+  PR A+RA I  VPEDRK QG+ L   +  N T+
Sbjct: 292 VARLVFGADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTL 351

Query: 361 NVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420
                 +RLG + +     VA A    + +K +  + PV  LSGGNQQKV LA+W     
Sbjct: 352 AKIRSISRLGFLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFHADC 411

Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480
            +LILDEPTRGVD+ AK EIY L++ LA  G A++VISSE  E+ GICDRVLVM EG I 
Sbjct: 412 DLLILDEPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAIV 471

Query: 481 GELAGAAITQENIMRLA 497
           GEL  +  T++ ++ LA
Sbjct: 472 GELTESKFTEQQLLTLA 488



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 60/229 (26%), Positives = 117/229 (51%), Gaps = 7/229 (3%)

Query: 24  DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83
           D+  ++R GE+  L G  G+G++ + +++ G    D G + L+G+P+ L  P  +  A I
Sbjct: 268 DVSFSVRAGEVVGLGGLVGSGRTEVARLVFGADKMDSGTVELNGKPLHLSSPREAVRARI 327

Query: 84  NLIYQEL---AVAPNISVAANVFMGSELRT--RLGLIDHAAMRSRTDAVLRQLGAGFGAS 138
            L+ ++     V  +  +  N  + +++R+  RLG +D    R    A+  ++     + 
Sbjct: 328 GLVPEDRKQQGVILDAPIRINTTL-AKIRSISRLGFLDAGKERQVAVALGAEMRLKASSV 386

Query: 139 DL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAII 197
           D     LS   QQ+V +A+       ++I+DEPT  +      +++N++  L   G AI+
Sbjct: 387 DAPVSSLSGGNQQKVALAKWFHADCDLLILDEPTRGVDVGAKGEIYNLINDLAKAGKAIL 446

Query: 198 YISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSE 246
            IS    E++ + DRV V+ +G+ VGEL   +   ++++ + + RS  E
Sbjct: 447 VISSEHQELFGICDRVLVMAEGAIVGELTESKFTEQQLLTLAMTRSARE 495


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: 736
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: 521
Length of database: 501
Length adjustment: 35
Effective length of query: 486
Effective length of database: 466
Effective search space:   226476
Effective search space used:   226476
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