Alignments for a candidate for mglA in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Jannaschia aquimarina GSW-M26

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_052500952.1 jaqu_RS12955 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_000877395.1:WP_052500952.1
          Length = 637

 Score =  338 bits (867), Expect = 3e-97
 Identities = 192/493 (38%), Positives = 298/493 (60%), Gaps = 6/493 (1%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L    + K F    AL+  S+   PGEV  ++G NGAGKSTL +I++G  QP  GEI 
Sbjct: 20  PLLMASGVSKSFGKTQALRDASLILRPGEVVGLLGANGAGKSTLSRIVSGHIQPSGGEIA 79

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
           ++G  +R     +A+  GI  V QE S+  +LSV ENIF+      G  + Y  M   A 
Sbjct: 80  FDGEALRLASTRDALGRGIALVAQETSLAPDLSVLENIFLPSLATPGR-LSYSAMRARAG 138

Query: 123 KFMKEEFGIEIDPEEK-LGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
           + +       I P  K +   S A +Q+VEIA+A+   A+++I DEPT+SL+  E ++LF
Sbjct: 139 EILAGLGHEHILPLHKEVRTLSAAQRQLVEIAKALSLDARLIIFDEPTASLSATEVDRLF 198

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTD-SIENLTKEKIVEMMVGR 240
           +V+  L++ G A+ F+SHRLEE+F I D+V+++R+G  +  D +  +LT+  I+E MVGR
Sbjct: 199 DVMARLRDGGRALAFVSHRLEEVFAITDRVTIIREGVSVAEDVATSSLTQGDIIEHMVGR 258

Query: 241 KLEKFY-IKEAHEPGEVVLEVKNLSG-ERFENVSFSLRRGEILGFAGLVGAGRTELMETI 298
            +   Y  +   E GE VLEV++L       +VSFS+RRGEILG  GLVGAGR+E +E I
Sbjct: 259 DIGAIYSARRPREAGETVLEVRSLRALPHVRDVSFSVRRGEILGLGGLVGAGRSEAVEAI 318

Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358
           +G RP++ GEI + GK  ++  P+DA+  G+G V EDR+   ++  +S+  N+ +  + +
Sbjct: 319 WGLRPRQAGEILVRGKPAKLRKPVDAVRAGMGFVAEDRRAQNIVPDLSVRENMLIALMGQ 378

Query: 359 IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILIL 418
             +G +  + R  +     I    +     D  +L  SGG QQK+++A+WL  +P ILIL
Sbjct: 379 -HRGFWRGYNRRADRMAALIADLGLPADRLDTSLLNYSGGMQQKIIIARWLLTEPDILIL 437

Query: 419 DEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDA 478
           DEPT+G+D+G ++ IYR++   A  G+ VI+ISS+  E+L +++R+ V+S G     + A
Sbjct: 438 DEPTKGVDIGTRSSIYRLLQDAADAGLAVIVISSDFEELLGLAERVVVVSDGLTIADLPA 497

Query: 479 KEASQEKVMKLAA 491
              ++EK+  LAA
Sbjct: 498 SRLTEEKLTLLAA 510



 Score = 90.5 bits (223), Expect = 2e-22
 Identities = 70/244 (28%), Positives = 125/244 (51%), Gaps = 14/244 (5%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +LEV+S+ +  P V   + VS     GE+  + G  GAG+S  ++ I G+     GEI+ 
Sbjct: 276 VLEVRSL-RALPHV---RDVSFSVRRGEILGLGGLVGAGRSEAVEAIWGLRPRQAGEILV 331

Query: 64  EGRGVRWNHPSEAINAGIVTVFQEL---SVMDNLSVAENIFMG-DEEKRGIFIDYKKMYR 119
            G+  +   P +A+ AG+  V ++    +++ +LSV EN+ +    + RG +  Y    R
Sbjct: 332 RGKPAKLRKPVDAVRAGMGFVAEDRRAQNIVPDLSVRENMLIALMGQHRGFWRGYN---R 388

Query: 120 EAEKF--MKEEFGIEIDP-EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKE 176
            A++   +  + G+  D  +  L  YS  +QQ + IAR +  +  +LILDEPT  +    
Sbjct: 389 RADRMAALIADLGLPADRLDTSLLNYSGGMQQKIIIARWLLTEPDILILDEPTKGVDIGT 448

Query: 177 TEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEM 236
              ++ +++   + G+A+I IS   EE+  + ++V V+ DG  I       LT+EK+  +
Sbjct: 449 RSSIYRLLQDAADAGLAVIVISSDFEELLGLAERVVVVSDGLTIADLPASRLTEEKLTLL 508

Query: 237 MVGR 240
              R
Sbjct: 509 AAPR 512


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: 733
Number of extensions: 34
Number of successful extensions: 9
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: 637
Length adjustment: 36
Effective length of query: 458
Effective length of database: 601
Effective search space:   275258
Effective search space used:   275258
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. 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