GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__Cola:Echvi_1282 Echvi_1282 ABC-type sugar
           transport system, ATPase component
          Length = 502

 Score =  404 bits (1039), Expect = e-117
 Identities = 221/497 (44%), Positives = 335/497 (67%), Gaps = 11/497 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +L VK+I K F GV AL  VS+E   G V AI+GENGAGKSTLMKI++GVY   +G I Y
Sbjct: 1   MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122
            G  V++ +  +A   GI  + QEL+++  LS+ ENIF+G E +  +  +D  KM++EA 
Sbjct: 61  NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           + +     + +DPE  + +  +  QQ+VEIA+A+  +++V+I+DEPTS+++ +E E LF 
Sbjct: 121 QLL-HRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFG 179

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           ++++L+ +G AI +ISH+L+E+F I D+  VLRDG+ I +  +E +T+E +++ MVGR++
Sbjct: 180 IIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI 239

Query: 243 EKFYIKEAHEPGEVVLEVKNLS------GERF--ENVSFSLRRGEILGFAGLVGAGRTEL 294
                    +  E VL VK+L+       ++F  ++++F L +GE+LG  GL+GAGRTEL
Sbjct: 240 VIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTEL 299

Query: 295 METIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLP 354
           ME +FG  P +G EI + GK  E   P +A++ G+ LVPEDRK+ GL+L M +  N SL 
Sbjct: 300 MEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLT 359

Query: 355 SLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPK 414
            +D I  G  +  K+EK LA   +    I+ +   + V  LSGGNQQKVVLAKWLA +PK
Sbjct: 360 VVDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRPK 419

Query: 415 ILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL-A 473
           +L+LDEPTRGID+ AK EIY+++ QLA EG+G+I++SSELPE+L +SDR+ VM+ G+L A
Sbjct: 420 VLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLTA 479

Query: 474 GIIDAKEASQEKVMKLA 490
            I    + S++++++ A
Sbjct: 480 NIPIDAQTSEDEILQAA 496



 Score = 97.1 bits (240), Expect = 1e-24
 Identities = 73/244 (29%), Positives = 120/244 (49%), Gaps = 12/244 (4%)

Query: 257 VLEVKNLSGE-----RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI 311
           +L VKN++ E       ++VS  L+ G +    G  GAG++ LM+ + G  P   G IY 
Sbjct: 1   MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60

Query: 312 EGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREK 371
            G  V+  +  DA E+GI ++ ++   L LI  +SI  N+ L        G     K  K
Sbjct: 61  NGDPVKFQNTRDAQEKGINIIHQE---LNLIPYLSIRENIFLGREPETPMGLLDVAKMHK 117

Query: 372 ELADWAIKT-FDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAK 430
           E A    +   ++ P  P   V  L  G QQ V +AK L+L+ +++I+DEPT  I     
Sbjct: 118 EAAQLLHRLKLNVDPETP---VSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEV 174

Query: 431 AEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLA 490
             ++ I+  L  EG  +  IS +L E+  ++DR  V+  GK+    + +  ++E +++  
Sbjct: 175 EILFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKM 234

Query: 491 AGLE 494
            G E
Sbjct: 235 VGRE 238


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: 655
Number of extensions: 32
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: 502
Length adjustment: 34
Effective length of query: 460
Effective length of database: 468
Effective search space:   215280
Effective search space used:   215280
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