GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pantoea rwandensis LMG 26275

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_084931811.1 HA51_RS03115 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_002095475.1:WP_084931811.1
          Length = 504

 Score =  385 bits (988), Expect = e-111
 Identities = 216/487 (44%), Positives = 316/487 (64%), Gaps = 12/487 (2%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           PL+ LR+I KTF G+ AL+  +L   AGEVHAL+GENGAGKSTLM++L G +T D  G  
Sbjct: 4   PLIELRDIVKTFGGIHALKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPD-SGTV 62

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
           +  G+ VQI GP++A   G+ +I+QE++LA  L+VAENI+L         +A   +    
Sbjct: 63  YDKGEAVQIKGPKAAMARGITLIHQEMALAQELTVAENIFLH---DLPTFIAWPKLRAKA 119

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
           A  L RLG +  PAA V  LS+A +Q+VEIARA+  +AR++V DEPT  LST + +RL  
Sbjct: 120 ANILRRLGFEIDPAATVGDLSVAHQQIVEIARALSQDARVIVFDEPTAVLSTQDANRLLE 179

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
           +I  LR  G+AI+YISHR+ E+  +ADR+T+++DG ++ T      +   ++++MVGR +
Sbjct: 180 IISDLRSVGVAIVYISHRLDEVFRIADRMTIMKDGQWIATESPQQTTLQEVIRLMVGRPV 239

Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311
              ++      +  EV L V  +   R+V+  SF +RAGEV+GL GLVG+GRTE+ARL+F
Sbjct: 240 DQLFSDRATYGMGEEV-LRVEKLNARRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIF 298

Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371
           GAD    G++ +      G  V+L +  P+QA+ AGIA + EDRK QG+ LD  +  N+ 
Sbjct: 299 GADRCDSGDIYL-----HGKKVSLRS--PQQAVKAGIALVPEDRKRQGVVLDMPIRANVT 351

Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431
           +         LG ++ +   +  ++    + ++ A     V +LSGGNQQKV+L++   +
Sbjct: 352 MANDKAVMAPLGFIHSSRETQVVSKLAQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNL 411

Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491
             +V+ILDEPTRGVD+GAK EIY+LI  LAQ G+A+++ISSE  E+ GLC+RVLVM EG 
Sbjct: 412 GGQVIILDEPTRGVDVGAKREIYQLIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGA 471

Query: 492 LAGEVRP 498
           + GE++P
Sbjct: 472 ICGELQP 478



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 59/228 (25%), Positives = 111/228 (48%), Gaps = 12/228 (5%)

Query: 27  RALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSA 86
           R +R V  +  AGEV  L G  G+G++ + +++ GA   D  G+ ++ G++V +  PQ A
Sbjct: 265 RKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIFGADRCD-SGDIYLHGKKVSLRSPQQA 323

Query: 87  RDLGVAVIYQE---------LSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLAR 137
              G+A++ ++         + +  N+++A +  +   L          +V   A  +  
Sbjct: 324 VKAGIALVPEDRKRQGVVLDMPIRANVTMANDKAVMAPLGFIHSSRETQVVSKLAQQMRL 383

Query: 138 LGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLR 197
             A     A V+SLS   +Q V +A+  +   +++++DEPT  +       ++ LI +L 
Sbjct: 384 KCAGLH--APVSSLSGGNQQKVVLAKWFNLGGQVIILDEPTRGVDVGAKREIYQLIAELA 441

Query: 198 GEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKM 245
            +GMA++ IS    E+  L +RV V+ +G   G L     S+  L+ M
Sbjct: 442 QQGMAVVVISSEHIELFGLCNRVLVMSEGAICGELQPDDYSEENLLSM 489


Lambda     K      H
   0.320    0.136    0.382 

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: 622
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: 540
Length of database: 504
Length adjustment: 35
Effective length of query: 505
Effective length of database: 469
Effective search space:   236845
Effective search space used:   236845
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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:

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