GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Gracilibacillus halophilus YIM-C55.5

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_040513205.1 J416_RS08125 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_000359605.1:WP_040513205.1
          Length = 506

 Score =  400 bits (1028), Expect = e-116
 Identities = 208/492 (42%), Positives = 321/492 (65%), Gaps = 3/492 (0%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L++  I K F G   L GV +E   GE+HA++GENGAGKSTLM I+ GVYQP++GEI 
Sbjct: 7   PVLQMSGIKKSFNGNEVLHGVDLEVKKGEIHALLGENGAGKSTLMNILGGVYQPNDGEIK 66

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEK-RGIFIDYKKMYREA 121
             G  +    P  +   GI  + QEL+V+ +L+V EN+F+G E + R  F+D K+M ++ 
Sbjct: 67  LSGAPIVMESPRVSQENGISFIHQELNVVTDLTVYENMFLGSEIRTRFGFLDVKEMCKQT 126

Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
           E+ +    G++IDP+  +     + +QM+EIA+++   + ++I+DEPT++LT+ E E+LF
Sbjct: 127 EEVLSR-LGVQIDPKTYVRDIETSYKQMIEIAKSLLHNSNMIIMDEPTTALTENEVERLF 185

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
             ++SL+  GV+II+ISH+L+EI  +CD+ +VLRDG  +GT  ++      I + MVG+ 
Sbjct: 186 AFMRSLQASGVSIIYISHKLKEIQTVCDRYTVLRDGHLVGTGEVKGTDLSAITQQMVGKS 245

Query: 242 LEKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300
           +           GE VL VK+L+ E  F +++FS+ +GE++GF GL G GRTEL E+IFG
Sbjct: 246 VSTNAFYHKATKGEPVLTVKHLTSEGLFNDINFSVSKGEVVGFTGLAGDGRTELFESIFG 305

Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360
           FR K GG I + G+ ++INHP  A++ GIGLVP++RK+  ++  +S++ N+SL SL   +
Sbjct: 306 FRKKYGGVIEVNGQPLKINHPRKAVQGGIGLVPKNRKENAIVKDLSVIENMSLSSLGHFE 365

Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420
               I  KRE++         +I+   P   +  LSGGNQQKVV+AKWL +   ++I D 
Sbjct: 366 ANGLIRSKREQKRFQEYKDQLNIKVHDPKVTIDSLSGGNQQKVVIAKWLEVDGDLIIFDN 425

Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480
           PT+GIDVGAK EIY+ +  LA+ G  +I++SSE PE+L++ DR+ +M  G++ G     E
Sbjct: 426 PTQGIDVGAKNEIYQHIMNLAEMGKAIIILSSEAPEILRVCDRVNIMFHGEITGKFTRDE 485

Query: 481 ASQEKVMKLAAG 492
            ++EK+M+ A G
Sbjct: 486 LTEEKIMEYATG 497



 Score =  100 bits (250), Expect = 9e-26
 Identities = 75/251 (29%), Positives = 127/251 (50%), Gaps = 17/251 (6%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           +P+L VK  H    G+     ++     GEV    G  G G++ L + I G  +   G I
Sbjct: 259 EPVLTVK--HLTSEGL--FNDINFSVSKGEVVGFTGLAGDGRTELFESIFGFRKKYGGVI 314

Query: 62  IYEGRGVRWNHPSEAINAGIVTV---FQELSVMDNLSVAENIFM---GDEEKRGIFIDYK 115
              G+ ++ NHP +A+  GI  V    +E +++ +LSV EN+ +   G  E  G+     
Sbjct: 315 EVNGQPLKINHPRKAVQGGIGLVPKNRKENAIVKDLSVIENMSLSSLGHFEANGLI---- 370

Query: 116 KMYREAEKFM--KEEFGIEI-DPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSL 172
           +  RE ++F   K++  I++ DP+  +   S   QQ V IA+ +     ++I D PT  +
Sbjct: 371 RSKREQKRFQEYKDQLNIKVHDPKVTIDSLSGGNQQKVVIAKWLEVDGDLIIFDNPTQGI 430

Query: 173 TQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEK 232
                 ++++ + +L E G AII +S    EI  +CD+V+++  GE  G  + + LT+EK
Sbjct: 431 DVGAKNEIYQHIMNLAEMGKAIIILSSEAPEILRVCDRVNIMFHGEITGKFTRDELTEEK 490

Query: 233 IVEMMVGRKLE 243
           I+E   G K E
Sbjct: 491 IMEYATGSKKE 501


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: 639
Number of extensions: 32
Number of successful extensions: 6
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: 506
Length adjustment: 34
Effective length of query: 460
Effective length of database: 472
Effective search space:   217120
Effective search space used:   217120
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 24 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