GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SM_b20673
          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.

Links

Downloads

Related tools

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:

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