Alignments for a candidate for xylG in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Sinorhizobium meliloti 1021

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Smeli:SM_b20503
          Length = 512

 Score =  414 bits (1063), Expect = e-120
 Identities = 210/494 (42%), Positives = 327/494 (66%), Gaps = 6/494 (1%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +LE++++ K F  V AL  V      GEVHA+ GENGAGKSTLM +IAGV QP EGE++ 
Sbjct: 6   VLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEVLI 65

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMG-DEEKRGIFIDYKKMYREAE 122
           EG  V+   P+ A + GI  V QE+++  + ++AEN+FM     +R   ++Y ++ R+A+
Sbjct: 66  EGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQLERDAQ 125

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
             M       ID  +K+G   I+ QQ+VEIA+A+    +VLI DEPT++LT+ E + LF 
Sbjct: 126 AVMNRL--APIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQVLFG 183

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           +++ LK +G++II+ISHR+ E+F +CD+V+V RDG Y+ T+ + ++T + +V +MVGR++
Sbjct: 184 IIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMVGREI 243

Query: 243 EKFYIKE---AHEPGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299
            + Y  +   +   GE +L V++L GERF +VSF LR GEILG  GL+G+GRTE+ E I 
Sbjct: 244 SQLYPDKQPSSERLGEPILSVRDLGGERFRDVSFELRYGEILGVGGLIGSGRTEIAEGIC 303

Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359
             RP   GEI +  K + +    DA + G+  + EDRK  G+ L +SI  N++   L  +
Sbjct: 304 ALRPVTQGEIRLHDKVLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSIAQNIAALDLKAL 363

Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419
                ++ + E+ LA+   +   +R    D  V  LSGGNQQKV +AK LA+ PK++++D
Sbjct: 364 TSLGLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIAKQLAVDPKVILMD 423

Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479
           EPTRGIDVGAK+EI+R++ +LA+ G+G+++ISSELPE++ + DR+ V+  G++AG +   
Sbjct: 424 EPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLVVREGRIAGEVSGN 483

Query: 480 EASQEKVMKLAAGL 493
           E ++E +M+LA+G+
Sbjct: 484 EMTEEVIMRLASGI 497



 Score = 93.6 bits (231), Expect = 1e-23
 Identities = 71/245 (28%), Positives = 117/245 (47%), Gaps = 11/245 (4%)

Query: 255 EVVLEVKNLSG-----ERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEI 309
           E VLE++N+S      +    V F L RGE+    G  GAG++ LM  I G      GE+
Sbjct: 4   ETVLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEV 63

Query: 310 YIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKR 369
            IEG  V+I  P  A   GI LV ++   + L    +I  N+ + + +R ++   +++ +
Sbjct: 64  LIEGAPVKIASPAVAQSLGIALVHQE---IALCPDATIAENMFMAATNR-RRSALMNYAQ 119

Query: 370 EKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGA 429
            +  A   +    + P    +KV  L   +QQ V +AK L L  ++LI DEPT  +    
Sbjct: 120 LERDAQAVMNR--LAPIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETE 177

Query: 430 KAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKL 489
              ++ I+  L   G+ +I IS  + EV  + DR+ V   G+        + + + V++L
Sbjct: 178 AQVLFGIIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRL 237

Query: 490 AAGLE 494
             G E
Sbjct: 238 MVGRE 242


Lambda     K      H
   0.318    0.138    0.385 

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: 624
Number of extensions: 26
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: 494
Length of database: 512
Length adjustment: 34
Effective length of query: 460
Effective length of database: 478
Effective search space:   219880
Effective search space used:   219880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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