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_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  340 bits (873), Expect = 5e-98
 Identities = 187/500 (37%), Positives = 301/500 (60%), Gaps = 9/500 (1%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M  ++E+K I K FPG+ A   V+++   GE+HA++GENGAGKSTLM ++ G+YQP++GE
Sbjct: 1   MSYVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGE 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           I+ +G+ V+   P+ A   GI  V Q   +++  +V ENI +G E   G  I+ KK  + 
Sbjct: 61  ILVKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKA 120

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
            E   K+ +G+ +DP  K+   S+ +QQ VEI + +Y+ A++LI DEPT++LT +E  +L
Sbjct: 121 VETISKQ-YGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITEL 179

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
            +++K L  +G +II I+H+L+EI E+CD+ +V+R G  IGT  I   T + +  MMVGR
Sbjct: 180 IQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGR 239

Query: 241 KLEKFYIKEAHEPGEVVLEVKNLSGERFENVS------FSLRRGEILGFAGLVGAGRTEL 294
           ++     K+  +P + VL++K+L  +   +++        +  GEILG AG+ G G+TEL
Sbjct: 240 EVNFSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTEL 299

Query: 295 METIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLP 354
           +E I G R   GG I + G+ +    P      G+G +P+DR K GL+L  ++  N+ L 
Sbjct: 300 IEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQ 359

Query: 355 SLDR--IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALK 412
           +  +        ++F    + A+  I+ +D+R          LSGGNQQK ++A+ +   
Sbjct: 360 TYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRS 419

Query: 413 PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472
           P +LI  +PTRG+DVGA   I+  + +   +G  V++IS EL EVL +SDRIAV+  GK+
Sbjct: 420 PDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKI 479

Query: 473 AGIIDAKEASQEKVMKLAAG 492
             I+DA + ++ ++  L AG
Sbjct: 480 VAIVDADKTNENELGLLMAG 499



 Score =  104 bits (259), Expect = 8e-27
 Identities = 72/243 (29%), Positives = 124/243 (51%), Gaps = 11/243 (4%)

Query: 257 VLEVKNLSGE-----RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI 311
           V+E+K++  E       +NV+  +++GEI    G  GAG++ LM  +FG      GEI +
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 312 EGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREK 371
           +GK V+I  P  A   GIG+V    +   L+   ++  N+ L        G  I+ K+  
Sbjct: 64  KGKPVKITDPNVANRLGIGMV---HQHFMLVEKFTVTENIILGK--EPTAGGKINIKKAA 118

Query: 372 ELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKA 431
           +  +   K + +    P  K+  +S G QQ+V + K L    +ILI DEPT  +      
Sbjct: 119 KAVETISKQYGLA-VDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEIT 177

Query: 432 EIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAA 491
           E+ +IM +L  EG  +I+I+ +L E++++ DR  V+  G+  G +D  E++ + +  +  
Sbjct: 178 ELIQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMV 237

Query: 492 GLE 494
           G E
Sbjct: 238 GRE 240



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 56/250 (22%), Positives = 125/250 (50%), Gaps = 10/250 (4%)

Query: 4   ILEVKS-IHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           +L++K  + K    + A+  + +E + GE+  + G +G G++ L++ I G+ +P  G I 
Sbjct: 256 VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQ 315

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQEL---SVMDNLSVAENIFMGDEEKRGI----FIDYK 115
             G+ +    P +   AG+  + Q+     ++ + +V ENI +    ++       +++ 
Sbjct: 316 LNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFN 375

Query: 116 KMYREAEKFMKEEFGIEIDPEEKLGK-YSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQ 174
           ++Y++A + + E++ +    E  L +  S   QQ   IAR V +   +LI  +PT  L  
Sbjct: 376 EIYKKANELI-EDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDV 434

Query: 175 KETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIV 234
              E +   +   ++KG A++ IS  L+E+  + D+++V+ +G+ +     +   + ++ 
Sbjct: 435 GAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELG 494

Query: 235 EMMVGRKLEK 244
            +M G   +K
Sbjct: 495 LLMAGGSAKK 504


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: 660
Number of extensions: 38
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: 509
Length adjustment: 34
Effective length of query: 460
Effective length of database: 475
Effective search space:   218500
Effective search space used:   218500
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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Protein sequences (fasta format)
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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