GapMind for catabolism of small carbon sources

 

Aligments 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_b20503 SM_b20503 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>lcl|FitnessBrowser__Smeli:SM_b20503 SM_b20503 sugar ABC transporter
           ATP-binding protein
          Length = 512

 Score =  432 bits (1112), Expect = e-125
 Identities = 227/515 (44%), Positives = 340/515 (66%), Gaps = 9/515 (1%)

Query: 1   MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60
           MT   +L++R + K FGA  AL+ +   +  GE+HAL GENGAGKSTLM V++GV  P +
Sbjct: 1   MTSETVLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSE 60

Query: 61  GEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM 120
           GE+L++G PV +  P  +++ GI L++QE+A+ P+ ++A N+FM +  R R  L+++A +
Sbjct: 61  GEVLIEGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQL 120

Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
                AV+ +L A    S   G L I+ QQ VEIA+AL    R++I DEPTAAL+E E +
Sbjct: 121 ERDAQAVMNRL-APIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQ 179

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
            LF ++R L+  G++IIYISHRMAEV++L DRVTV RDG +V   +  ++  + +V++MV
Sbjct: 180 VLFGIIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMV 239

Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 300
           GR +S+ Y  ++  P+       ++ VR L G + R  SF++R GE+LG  GL+G+GRTE
Sbjct: 240 GREISQLYPDKQ--PSSERLGEPILSVRDLGGERFRDVSFELRYGEILGVGGLIGSGRTE 297

Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360
           +A  +    P + G+I L  + + + +   A +AG+ Y+ EDRKG G+FL +++A N   
Sbjct: 298 IAEGICALRPVTQGEIRLHDKVLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSIAQNIAA 357

Query: 361 NVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420
                 T LGL+ SR    +A    +RL V++   + PV  LSGGNQQKV +A+ L + P
Sbjct: 358 LDLKALTSLGLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIAKQLAVDP 417

Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480
           KV+++DEPTRG+D+ AKSEI++L+  LA  G+ ++VISSELPE+IG+CDRVLV+REG I 
Sbjct: 418 KVILMDEPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLVVREGRIA 477

Query: 481 GELAGAAITQENIMRL------ATDTNVPRTAPAS 509
           GE++G  +T+E IMRL      AT+TN+  +  A+
Sbjct: 478 GEVSGNEMTEEVIMRLASGIGPATETNLKASGHAA 512



 Score = 98.6 bits (244), Expect = 5e-25
 Identities = 74/256 (28%), Positives = 123/256 (48%), Gaps = 13/256 (5%)

Query: 263 TVMQVRAL-----AGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDIL 317
           TV+++R +     A   +    F +  GEV    G  GAG++ L  ++ G    S G++L
Sbjct: 5   TVLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEVL 64

Query: 318 LEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSL 377
           +EG PV I  P  A   GIA V ++     L     +A N  M   +R  R  L+    L
Sbjct: 65  IEGAPVKIASPAVAQSLGIALVHQEI---ALCPDATIAENMFMAATNRR-RSALMNYAQL 120

Query: 378 GGVARAAIQRLN-VKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYA 436
              A+A + RL  + V+     VG L   +QQ V +A+ L +  +VLI DEPT  +    
Sbjct: 121 ERDAQAVMNRLAPIDVSQK---VGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETE 177

Query: 437 KSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRL 496
              ++ ++  L ++G++++ IS  + EV  +CDRV V R+G        + +T ++++RL
Sbjct: 178 AQVLFGIIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRL 237

Query: 497 ATDTNVPRTAPASHSS 512
                + +  P    S
Sbjct: 238 MVGREISQLYPDKQPS 253


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: 707
Number of extensions: 37
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: 512
Length adjustment: 35
Effective length of query: 486
Effective length of database: 477
Effective search space:   231822
Effective search space used:   231822
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:

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:

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:

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, or view the source code.

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