GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Methanosarcina acetivorans C2A

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 WP_011022097.1 MA_RS10955 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_000007345.1:WP_011022097.1
          Length = 267

 Score =  112 bits (279), Expect = 2e-29
 Identities = 80/250 (32%), Positives = 129/250 (51%), Gaps = 14/250 (5%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M+ IL VKS+ K+F  + A+KG+S +   G + A +G NGAGKST +K++  V +P  GE
Sbjct: 1   MQNILSVKSLTKKFDDLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGE 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           I+  G            + GI  VFQ+ S+   L+  EN+     E   +     K  RE
Sbjct: 61  ILINGYNALKEQDKARSSFGI--VFQDYSLDSELTAYENM-----EYHSVIYKVPKAERE 113

Query: 121 AE-KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179
              K   E  G+     + + KYS  +++ +EIARA+    KVL LDEPT  L  +    
Sbjct: 114 ERIKTALEIVGLWNRRNDLVKKYSGGMKRRLEIARALVHYPKVLFLDEPTVGLDPQTRMS 173

Query: 180 LFEVVKSLKEKGVAIIFI-SHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           ++  +K L E+    IF+ +H ++E   + DK++++  G+      IE+ T  +I+E   
Sbjct: 174 IWNHIKRLNEERKMTIFLTTHYMDEAEAMADKIAIIDHGKI-----IESGTLAEIMERTE 228

Query: 239 GRKLEKFYIK 248
              LE+ ++K
Sbjct: 229 TESLEESFLK 238



 Score = 61.2 bits (147), Expect = 4e-14
 Identities = 67/251 (26%), Positives = 116/251 (46%), Gaps = 33/251 (13%)

Query: 257 VLEVKNLSGERFEN------VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIY 310
           +L VK+L+ ++F++      +SF +  G I  F G  GAG++  ++ +        GEI 
Sbjct: 4   ILSVKSLT-KKFDDLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGEIL 62

Query: 311 IEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKRE 370
           I G         D      G+V +D     L   ++   N+   S         + +K  
Sbjct: 63  INGYNALKEQ--DKARSSFGIVFQD---YSLDSELTAYENMEYHS---------VIYKVP 108

Query: 371 KELADWAIKT-FDIRPAYPDRKVLY--LSGGNQQKVVLAKWLALKPKILILDEPTRGIDV 427
           K   +  IKT  +I   +  R  L    SGG ++++ +A+ L   PK+L LDEPT G+D 
Sbjct: 109 KAEREERIKTALEIVGLWNRRNDLVKKYSGGMKRRLEIARALVHYPKVLFLDEPTVGLDP 168

Query: 428 GAKAEIYRIMSQLAKEGVGVIMISSE-LPEVLQMSDRIAVMSFGK------LAGIIDAKE 480
             +  I+  + +L +E    I +++  + E   M+D+IA++  GK      LA I++  E
Sbjct: 169 QTRMSIWNHIKRLNEERKMTIFLTTHYMDEAEAMADKIAIIDHGKIIESGTLAEIMERTE 228

Query: 481 AS--QEKVMKL 489
               +E  +KL
Sbjct: 229 TESLEESFLKL 239


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: 353
Number of extensions: 18
Number of successful extensions: 5
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: 267
Length adjustment: 29
Effective length of query: 465
Effective length of database: 238
Effective search space:   110670
Effective search space used:   110670
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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