GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA 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_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__Smeli:SM_b20673 SM_b20673 sugar uptake ABC
           transporter ATP-binding protein
          Length = 526

 Score =  415 bits (1066), Expect = e-120
 Identities = 229/502 (45%), Positives = 334/502 (66%), Gaps = 13/502 (2%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           +PIL  ++I K F GV ALK V  E   GE+HA++GENGAGKSTLMK+++GVY   EG +
Sbjct: 16  RPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEGAV 75

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEK-RGIFIDYKKMYRE 120
             +G  VR+++  +A  AGI  + QEL+++  L VA+NIF+G E    G+F+D +K   E
Sbjct: 76  RVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVD-RKASLE 134

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A + +    GIE+DPE ++G+  +  QQ+VEIA+A+  +A++LI+DEPTS+L+  E  +L
Sbjct: 135 AARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRRL 194

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F++++ L   GV II+ISHR++E+ ++ D+V+V RDG ++    +  L +  I+  MVGR
Sbjct: 195 FKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTIIAAMVGR 254

Query: 241 KLEKFYIKEAHE-PGEVVLEVKNLS---------GERFENVSFSLRRGEILGFAGLVGAG 290
            L   + ++  +  GE VL V++LS          +  + VSF +R GEILG  GL+GAG
Sbjct: 255 NLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAG 314

Query: 291 RTELMETIFGFRP-KRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMH 349
           RTE++ETIF      RGGEI ++G  V I  P DA   G  LV EDRK  GL L  SI  
Sbjct: 315 RTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRD 374

Query: 350 NVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWL 409
           NV+LP + R+ +    SF+ E+ LA  A+    +R A   +    LSGGNQQKVV+ KWL
Sbjct: 375 NVALPLVGRLARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIGKWL 434

Query: 410 ALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSF 469
           A  P++L+LDEPTRGIDVGAK EIY ++ +LA +G+ ++++SSELPE+L ++DRI VM+ 
Sbjct: 435 ATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAE 494

Query: 470 GKLAGIIDAKEASQEKVMKLAA 491
           G+  G+I  +EAS+E++M+LAA
Sbjct: 495 GRQTGLISREEASEERIMQLAA 516



 Score = 73.9 bits (180), Expect = 1e-17
 Identities = 63/249 (25%), Positives = 115/249 (46%), Gaps = 10/249 (4%)

Query: 2   KPILEVKSIHKRFPGVHA----LKGVSMEFYPGEVHAIVGENGAGKSTLMK-IIAGVYQP 56
           +P+L V+ +     G H     LKGVS +   GE+  I G  GAG++ +++ I A     
Sbjct: 270 EPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAGRTEILETIFASNEGL 329

Query: 57  DEGEIIYEGRGVRWNHPSEAINAGIVTVFQELSVMD---NLSVAENIFMGDEEKRGIF-I 112
             GEI  +G  V    P +A   G   V ++        + S+ +N+ +    +   F +
Sbjct: 330 RGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRDNVALPLVGRLARFGL 389

Query: 113 DYKKMYREAEKFMKEEFGIEI-DPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSS 171
              +  R   K   +  G+      +  G  S   QQ V I + +    +VL+LDEPT  
Sbjct: 390 RSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIGKWLATGPRVLLLDEPTRG 449

Query: 172 LTQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKE 231
           +      ++++++  L   G+AI+ +S  L E+  + D++ V+ +G   G  S E  ++E
Sbjct: 450 IDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAEGRQTGLISREEASEE 509

Query: 232 KIVEMMVGR 240
           +I+++   R
Sbjct: 510 RIMQLAAPR 518


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: 703
Number of extensions: 43
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: 526
Length adjustment: 34
Effective length of query: 460
Effective length of database: 492
Effective search space:   226320
Effective search space used:   226320
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:

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