GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Azospirillum brasilense Sp245

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 AZOBR_RS06950 AZOBR_RS06950 ABC transporter

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__azobra:AZOBR_RS06950
          Length = 520

 Score =  291 bits (744), Expect = 5e-83
 Identities = 183/499 (36%), Positives = 270/499 (54%), Gaps = 15/499 (3%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           LE++ I KRFPG  A   V +   PGE+HA++GENGAGKSTL+KII GV   D G I + 
Sbjct: 13  LELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWN 72

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124
           G       P+ A   GI  VFQ  S+ D L+VAENI +G ++   I        R AE  
Sbjct: 73  GHDTHIPDPAGARRLGIGMVFQHFSLFDTLTVAENISLGLDQPGPIDA---LSARIAE-- 127

Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184
           + E +G+ +DP   +   S+  +Q VEI R + +  K+LI+DEPTS LT +E  +LFE +
Sbjct: 128 VSERYGLSLDPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFETL 187

Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEK 244
           + L  +G  I++ISH+LEEI  +CD  +VLR G  +G+      T   + EMM+G +L  
Sbjct: 188 RRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETARSLAEMMIGTELST 247

Query: 245 FYIKEAHEPGEVVLEVKNLS-------GERFENVSFSLRRGEILGFAGLVGAGRTELMET 297
                  E G   L+V++LS           ++VSF +R GEILG AG+ G G+ ELM  
Sbjct: 248 PERLPQGEAGAAKLQVRHLSTTSDNPFATNLKDVSFEVRAGEILGIAGVAGNGQAELMAA 307

Query: 298 IFG-FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
           + G         + IEG+      P +    G+  VPE+R   G +  +S+  N  L   
Sbjct: 308 LSGEALVPDPASVAIEGRPAGHLGPRERRLLGLAFVPEERLGRGAVPELSLSENALLSGY 367

Query: 357 DR--IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPK 414
            R  + +   + F R +  A+  I  F++       +   LSGGN QK ++ + +  KP+
Sbjct: 368 AREPLVRSGLVHFGRARSYAERIIGAFNVVTHGHRAEARSLSGGNLQKFIIGREILQKPR 427

Query: 415 ILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAG 474
           +L++ +PT G+D GA A I+R +  LA+ G  V++IS +L E+  +SDRIAV+  G L+ 
Sbjct: 428 LLVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELFVLSDRIAVLFHGHLSE 487

Query: 475 IIDAKEASQEKVMKLAAGL 493
                  S E++  L  GL
Sbjct: 488 SRPTHHTSVEEIGLLMGGL 506



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 66/227 (29%), Positives = 108/227 (47%), Gaps = 12/227 (5%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328
           + V   LR GEI    G  GAG++ L++ I+G      G I   G    I  P  A   G
Sbjct: 29  DQVDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWNGHDTHIPDPAGARRLG 88

Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFK-REKELADWAIKTFDIRPAY 387
           IG+V +      L   +++  N+SL  LD+   GP  +   R  E+++    + D     
Sbjct: 89  IGMVFQH---FSLFDTLTVAENISL-GLDQ--PGPIDALSARIAEVSERYGLSLD----- 137

Query: 388 PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGV 447
           P R V  LS G +Q+V + + L   PK+LI+DEPT  +       ++  + +LA EG  +
Sbjct: 138 PRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFETLRRLAAEGCTI 197

Query: 448 IMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           + IS +L E+  + D   V+  G++ G  D +  +   + ++  G E
Sbjct: 198 LYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETARSLAEMMIGTE 244


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: 617
Number of extensions: 31
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: 494
Length of database: 520
Length adjustment: 34
Effective length of query: 460
Effective length of database: 486
Effective search space:   223560
Effective search space used:   223560
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:

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