GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcA in Herbaspirillum seropedicae SmR1

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05250 HSERO_RS05250 D-ribose
           transporter ATP binding protein
          Length = 520

 Score =  407 bits (1046), Expect = e-118
 Identities = 232/517 (44%), Positives = 332/517 (64%), Gaps = 15/517 (2%)

Query: 5   SDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT 64
           + +S+  P++ALRN+CK FPGV AL   +    AGEVHALMGENGAGKSTLMKILSG Y 
Sbjct: 14  ASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQ 73

Query: 65  ADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GL-V 122
            D  G+  +DG+ V+I  P+ A+ LG+ +I+QEL+L  +LS A+NI++GR  ++  GL +
Sbjct: 74  RD-SGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI 132

Query: 123 ARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLS 182
              ++ R  A   AR+  D  P+  V  L++A++Q+VEIA+A+ F++R+L+MDEPT  L+
Sbjct: 133 DEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192

Query: 183 THETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAAL 242
             E   LF +IR L+ +G+ I+YISH+M E+ ++ADRV+V+RDG ++ T+     S   +
Sbjct: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252

Query: 243 VKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAG 302
           + MMVGR L G   +        +V+L VR +  GR ++  SF LR GE+LG AGL+GAG
Sbjct: 253 ISMMVGRALDG-EQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAG 311

Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362
           RTE+AR +FGAD    GE+ I      GG   + +  P  A+  GI YL+EDRK  GL +
Sbjct: 312 RTEVARAIFGADPLEAGEIII-----HGGKAVIKS--PADAVAHGIGYLSEDRKHFGLAV 364

Query: 363 DQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422
              V  NI L    R    +G +++ A R      +  L I+    +     LSGGNQQK
Sbjct: 365 GMDVQANIALSSMGR-FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQK 423

Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482
           +++++ L     +L  DEPTRG+D+GAKSEIY+L++ALA+ G AI+MISSELPEV+ +  
Sbjct: 424 IVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSH 483

Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAA 519
           RVLVM EG + GE+  A +   TQE+I+ LAT   +A
Sbjct: 484 RVLVMCEGRITGELARADA---TQEKIMQLATQRESA 517


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: 614
Number of extensions: 30
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 540
Length of database: 520
Length adjustment: 35
Effective length of query: 505
Effective length of database: 485
Effective search space:   244925
Effective search space used:   244925
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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