GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas simiae WCS417

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__WCS417:GFF3463
          Length = 502

 Score =  354 bits (909), Expect = e-102
 Identities = 217/513 (42%), Positives = 309/513 (60%), Gaps = 25/513 (4%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           LL L NICK +PGV+AL+ + L    GE+HAL+GENGAGKSTLMKIL G    D G +  
Sbjct: 4   LLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEG-QIL 62

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRAC 131
           IDGQ  Q    + A   G+ +++QE SL P L+  ENI+LG  L  R GL+ + +MV A 
Sbjct: 63  IDGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVEAS 122

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
                RLG        V  LS+A++Q VEIA+A+  +AR+LV+DEPT  L+  E + LF 
Sbjct: 123 EALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFE 182

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
           ++R+L+ +G+A+++ISH + EI ++ DR++VLRDG  VG  D A      LV+MMVGR L
Sbjct: 183 IMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGRRL 242

Query: 252 SGFY----TKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307
           +  +    T+  G      ++L V+D+   R      F L  GE+LG AGLVG+GRTELA
Sbjct: 243 ACSFPPKPTRERG-----PLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTELA 297

Query: 308 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 367
             + GA      +V +      G  +TL    P QA+  GI  L E RK +GL  D S+ 
Sbjct: 298 LGMMGALPSVSKDVWL-----RGEKITL--DDPAQALAHGIGLLPESRKSEGLITDFSIR 350

Query: 368 ENINL--IVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVML 425
           ENI+L  +   ++A GL   NR  A       +  L I+   ++  V  LSGGNQQKV++
Sbjct: 351 ENISLNNLPKYQNASGLIDKNRECA--SVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVI 408

Query: 426 SRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVL 485
           +R +     VL+ DEPTRG+D+GAK++IY L+ +L + G AI+MISSELPE++G+CDRV 
Sbjct: 409 ARWINHHCDVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVA 468

Query: 486 VMREGTLAGEVRPAGSAAETQERIIALATGAAA 518
           V  +G +   V+   ++A   + ++  ATG ++
Sbjct: 469 VFHKGAI---VKLLEASAVNPQEVMRHATGGSS 498


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: 576
Number of extensions: 28
Number of successful extensions: 8
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