Alignments for a candidate for mglA in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Pantoea rwandensis LMG 26275

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_084932744.1 HA51_RS05190 ribose ABC transporter ATP-binding protein RbsA

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_002095475.1:WP_084932744.1
          Length = 502

 Score =  433 bits (1114), Expect = e-126
 Identities = 220/491 (44%), Positives = 331/491 (67%), Gaps = 4/491 (0%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           LL++ GI KSFPGVKAL+  +L V P  + AL+GENGAGKST++K L GIY  D+G++ +
Sbjct: 4   LLQLKGIEKSFPGVKALNGASLAVYPGRVMALVGENGAGKSTMMKVLTGIYSMDAGSLQW 63

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGR-YPTKGMFVDQDKMYRETK 131
            GK++ F   K + E GI ++HQELNL+ Q +V +N++LGR +  +   ++ ++MY E  
Sbjct: 64  LGKDVAFSGPKASQEAGIGIIHQELNLIPQLTVAENIFLGREFVNRFGRIEWNRMYAEAD 123

Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
           A+   L++  +    VG LS+   QM+EIAK  S+ ++++IMDEPT +LT+ E   LF +
Sbjct: 124 ALLHRLNLRFNSHKLVGDLSIGDQQMVEIAKVLSFESQVIIMDEPTDALTDTETLSLFRV 183

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251
           I +LK +GCGIVYISH+M+EIF++CD+VTV RDGQ+IA   ++ L+ + +I MMVGR L 
Sbjct: 184 INELKAQGCGIVYISHRMKEIFEICDDVTVFRDGQFIAERAVSDLSEESLIEMMVGRKLE 243

Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
            ++P  +  PG++ L V +L+    P + +VSF+L KGEILGI+GL+GA RT++++ L+G
Sbjct: 244 DQYPHIDQAPGDIRLTVEHLSG---PGVDNVSFNLRKGEILGISGLMGAGRTELMKVLYG 300

Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371
              +S GT+TL+G++I   +  + + +G   ++E+R+  G+   + +  N  ++ +R + 
Sbjct: 301 ALPRSKGTVTLNGREIMTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360

Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
           +  G L +S  +      I    VKTP     IG LSGGNQQKV I R L+T+P +L+LD
Sbjct: 361 HATGNLKHSEEQLAVGDFIRLFNVKTPSMEQPIGLLSGGNQQKVAIARGLMTRPNVLILD 420

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EPTRG+DVGAK EIYQLI +   +G  II++SSEMPE+LG++DRILVM  G +SG    +
Sbjct: 421 EPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSRE 480

Query: 492 TTTQNEILRLA 502
             TQ  ++  A
Sbjct: 481 QATQESLMAAA 491



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 64/234 (27%), Positives = 106/234 (45%), Gaps = 10/234 (4%)

Query: 22  SFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHS 81
           S PGV   DNV+  +R   I  + G  GAG++ L+K L+G   +  GT+   G+EI   S
Sbjct: 264 SGPGV---DNVSFNLRKGEILGISGLMGAGRTELMKVLYGALPRSKGTVTLNGREIMTRS 320

Query: 82  AKEALENGISMVHQELN---LVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAIFDELD 138
            ++ L NGI  + ++     LVL  SV +NM L             K   E  A+ D + 
Sbjct: 321 PQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSHATGNLKHSEEQLAVGDFIR 380

Query: 139 I----DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRK 194
           +           +G LS    Q + IA+       ++I+DEPT  +       ++ +I +
Sbjct: 381 LFNVKTPSMEQPIGLLSGGNQQKVAIARGLMTRPNVLILDEPTRGVDVGAKKEIYQLINQ 440

Query: 195 LKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGR 248
            K  G  I+ +S +M E+  + D + V+ +G           T + ++A  VG+
Sbjct: 441 FKAEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSREQATQESLMAAAVGK 494


Lambda     K      H
   0.318    0.136    0.384 

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: 608
Number of extensions: 27
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: 506
Length of database: 502
Length adjustment: 34
Effective length of query: 472
Effective length of database: 468
Effective search space:   220896
Effective search space used:   220896
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.

Downloads

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

Related tools

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