Alignments for a candidate for mglA in Alkalihalobacterium alkalinitrilicum DSM 22532

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Alkalihalobacterium alkalinitrilicum DSM 22532

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_078427229.1 BK574_RS01730 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_002019605.1:WP_078427229.1
          Length = 503

 Score =  352 bits (903), Expect = e-101
 Identities = 197/475 (41%), Positives = 300/475 (63%), Gaps = 8/475 (1%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +LE+  ++K F G HALK ++++   GEVH++VGENGAGKSTL+KI+ GVYQP  G I +
Sbjct: 3   LLEIDQLNKHFGGNHALKDITLKIKAGEVHSLVGENGAGKSTLIKIVTGVYQPTNGTIKW 62

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE---EKRGIFIDYKKMYRE 120
           E   V+   P  A   GI  + Q+  ++   +  EN+F+  +   +K GI ID+  M ++
Sbjct: 63  ENEKVKVQTPKAAQQLGINVIHQDRQLVPYFTGLENLFLNQDYPKKKFGIGIDWNAMKQQ 122

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A+  ++EE+GI++     +   S + + ++EI RA+  ++K+LILDEPT++LT KE+E L
Sbjct: 123 ADA-LQEEWGIQLPLSTLVSNMSPSERTLLEILRAMMMESKLLILDEPTAALTDKESELL 181

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F  ++ LKEKGVAI+++SHRLEE+ ++ D+V+VL  G+   T + + L+KE I+E M G 
Sbjct: 182 FSFIRRLKEKGVAIVYVSHRLEEVIQLSDQVTVLIGGKIATTLTKKELSKETIIEYMTGG 241

Query: 241 KLEKFYIKEAHEPG--EVVLEVKNLS--GERFENVSFSLRRGEILGFAGLVGAGRTELME 296
           K  K   + + E    +++L VK L    +  ++V   L +GEILG  GL GAGRTEL+E
Sbjct: 242 KAIKALKERSDEKRSEQILLSVKGLKTKDQVVKSVDLQLHKGEILGIYGLAGAGRTELLE 301

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            I+G R    G I  E   +E   P  +IE G+ L+PE+R    LI+  +I  N++LP L
Sbjct: 302 AIYGLRKIEAGSIQFENNVIEKISPNKSIENGVVLIPENRHDDALIMGNTIRENMTLPIL 361

Query: 357 DRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416
             + K   I  K+E +  +  ++ F ++    ++ V  LSGGNQQKVV AK L  +P I 
Sbjct: 362 SDLTKRGVIQRKQEFQFVEQEMERFKVKATGSEQTVSELSGGNQQKVVFAKALLCQPTIY 421

Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471
           + DEPT+ +DV  +AEI+R +   A EG G+I +SS+LPEVL++SDRI VM+ G+
Sbjct: 422 LCDEPTQAVDVMTRAEIHRFLQNQADEGKGIIFVSSDLPEVLEISDRIVVMNEGE 476



 Score = 87.0 bits (214), Expect = 1e-21
 Identities = 57/225 (25%), Positives = 118/225 (52%), Gaps = 5/225 (2%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328
           ++++  ++ GE+    G  GAG++ L++ + G      G I  E ++V++  P  A + G
Sbjct: 20  KDITLKIKAGEVHSLVGENGAGKSTLIKIVTGVYQPTNGTIKWENEKVKVQTPKAAQQLG 79

Query: 329 IGLVPEDRKKLGLILIMSIMHNVSL-PSLDRIKKGPFISFKREKELADWAIKTFDIRPAY 387
           I ++ +DR+   L+   + + N+ L     + K G  I +   K+ AD   + + I+   
Sbjct: 80  INVIHQDRQ---LVPYFTGLENLFLNQDYPKKKFGIGIDWNAMKQQADALQEEWGIQLPL 136

Query: 388 PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGV 447
               V  +S   +  + + + + ++ K+LILDEPT  +       ++  + +L ++GV +
Sbjct: 137 -STLVSNMSPSERTLLEILRAMMMESKLLILDEPTAALTDKESELLFSFIRRLKEKGVAI 195

Query: 448 IMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           + +S  L EV+Q+SD++ V+  GK+A  +  KE S+E +++   G
Sbjct: 196 VYVSHRLEEVIQLSDQVTVLIGGKIATTLTKKELSKETIIEYMTG 240



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 60/232 (25%), Positives = 122/232 (52%), Gaps = 11/232 (4%)

Query: 20  LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINA 79
           +K V ++ + GE+  I G  GAG++ L++ I G+ + + G I +E   +    P+++I  
Sbjct: 273 VKSVDLQLHKGEILGIYGLAGAGRTELLEAIYGLRKIEAGSIQFENNVIEKISPNKSIEN 332

Query: 80  GIVTV----FQELSVMDNLSVAENI---FMGDEEKRGIFIDYKKMYREAEKFMKEEFGIE 132
           G+V +      +  +M N ++ EN+    + D  KRG+ I  K+ ++  E+ M E F ++
Sbjct: 333 GVVLIPENRHDDALIMGN-TIRENMTLPILSDLTKRGV-IQRKQEFQFVEQEM-ERFKVK 389

Query: 133 ID-PEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKG 191
               E+ + + S   QQ V  A+A+  +  + + DEPT ++      ++   +++  ++G
Sbjct: 390 ATGSEQTVSELSGGNQQKVVFAKALLCQPTIYLCDEPTQAVDVMTRAEIHRFLQNQADEG 449

Query: 192 VAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243
             IIF+S  L E+ EI D++ V+ +GE +      +L   +++++    K E
Sbjct: 450 KGIIFVSSDLPEVLEISDRIVVMNEGETVAELVNHHLQPNEVLDICYRFKKE 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: 696
Number of extensions: 32
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 494
Length of database: 503
Length adjustment: 34
Effective length of query: 460
Effective length of database: 469
Effective search space:   215740
Effective search space used:   215740
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources