GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF3463 PS417_17730
           ribonucleotide-diphosphate reductase subunit alpha
          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.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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