GapMind for catabolism of small carbon sources

 

Alignments 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_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__HerbieS:HSERO_RS05320
          Length = 502

 Score =  368 bits (945), Expect = e-106
 Identities = 225/506 (44%), Positives = 298/506 (58%), Gaps = 13/506 (2%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           +L L  I K F  V  LR V+L   AGEVHAL+GENGAGKSTLMKIL G    D  GE  
Sbjct: 1   MLQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPD-AGEIR 59

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRAC 131
           IDGQ  + D  ++A   GV V++QE SL P L   +N++L R L+ R G + R  M R  
Sbjct: 60  IDGQPCRFDSYRAAIAGGVGVVFQEFSLIPYLDAVDNMFLARELRSRWGWLQRAAMRRRA 119

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
              + +LG        V  LS+AQ+Q VEIA+A+  +ARILV+DEPT  L+  E + LFA
Sbjct: 120 QEIIGQLGVAIPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHLFA 179

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
           ++R LR +G+AI++ISH + EI E+ DR+TVLRDG +V T   A + QA LV+MMVGR +
Sbjct: 180 VMRSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVEMMVGRRI 239

Query: 252 SGFYTK--THGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARL 309
              +      G   E EV+L V  +   R+     F LR GE+LG AGLVG+GRTE    
Sbjct: 240 ENCFPPKPAKGGEGEGEVVLEVHALQLRRQAPVSQFQLRRGEILGFAGLVGSGRTETVLA 299

Query: 310 VFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHEN 369
           + GA A    ++ +         V L    P QA+ AGI  L E RK QGL    S+  N
Sbjct: 300 MLGAHAALSCKLSMHG-------VPLRFADPAQALQAGIGLLPESRKEQGLITSFSILHN 352

Query: 370 INLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLL 429
           ++L    +  LG   L+R   ++ T  A+  + ++   AQV V  LSGGNQQKV+++R +
Sbjct: 353 VSLNNYGKYRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVRVDTLSGGNQQKVVIARWI 412

Query: 430 EIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMRE 489
               +VLI DEPTRG+D+GAKSEIY+L+      G +ILMISSELPEVVG+ DRV V R 
Sbjct: 413 NHAMKVLIFDEPTRGIDVGAKSEIYQLMREFTAQGYSILMISSELPEVVGMADRVCVFRG 472

Query: 490 GTLAGEVRPAGSAAETQERIIALATG 515
           G +   +   G A   +E +    TG
Sbjct: 473 GGIVATLE--GEAVNAEEIMTHATTG 496


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: 643
Number of extensions: 29
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 540
Length of database: 502
Length adjustment: 35
Effective length of query: 505
Effective length of database: 467
Effective search space:   235835
Effective search space used:   235835
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:

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