GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupC in Shewanella oneidensis MR-1

Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate 203375 SO4296 NupC family protein (NCBI ptt file)

Query= uniprot:A0KU05
         (419 letters)



>FitnessBrowser__MR1:203375
          Length = 401

 Score =  398 bits (1023), Expect = e-115
 Identities = 201/418 (48%), Positives = 292/418 (69%), Gaps = 20/418 (4%)

Query: 3   ILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVSDA 62
           ++ S++G+ VLL +G L S+N+  I+ R V GA  I  A   FVL   +G D+L +VS+ 
Sbjct: 1   MIQSILGIFVLLGVGLLFSDNRSLISWRAVIGAFGIIIALAFFVLATEIGADVLLAVSNT 60

Query: 63  VSSVIGYAQNGIGFLFGDLANFK---LGFIFAVNVLPVIVFFSSLIAVLYYLGIMQWIIR 119
           V  V GY   GI F FG L NF    +GF++A+ VLP I+F ++L ++LYYLGIMQW + 
Sbjct: 61  VGKVFGYGTEGIKFAFGSLVNFSVEGIGFVWALQVLPQIIFTAALTSLLYYLGIMQWFVL 120

Query: 120 IIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAG 179
           IIGG LQK LGTSR ESM+A  NI +GQTEAPL+++P+   +T++++FA+MVGGL+SIAG
Sbjct: 121 IIGGSLQKVLGTSRAESMNAAGNIILGQTEAPLLIKPYHRVLTRAQIFAVMVGGLSSIAG 180

Query: 180 SVLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKNDMDELPEDPDKPANVLD 239
           S+LAG A MGV + YL+ A FM+AP GL+ AKL+ PETE   N++ ELP+D +KP++ +D
Sbjct: 181 SILAGLAGMGVALNYLIMACFMSAPAGLMFAKLLIPETEPTVNEVPELPDD-EKPSSFID 239

Query: 240 AAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGVEGLTLELILGYIFMPLA 299
           A A GA +GM +A  VGA+++A +GL+A++NG +G +G  FG+  LT+++ILG +F P+A
Sbjct: 240 AIAKGAIAGMGIAAIVGAVIIACIGLMALLNGGLGAIGELFGMPTLTVDMILGTLFAPVA 299

Query: 300 FLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGGMIVADTGLAMTDRTKAI 359
           +LIG+PW EA  AG+F+GQKI +NEFVA+ N                   + ++ R+ AI
Sbjct: 300 WLIGIPWVEASTAGAFLGQKIAMNEFVAFANMG----------------NVELSARSNAI 343

Query: 360 ISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAGSLANLMSATIAGLFL 417
           ++ ALCGFAN+ S+A++ G L  M P R   + +LG++ ++A +LANLM+A I  LF+
Sbjct: 344 MTIALCGFANIGSVAMVCGALSKMIPQRAGLIGQLGMKVLLAATLANLMNAAIVSLFI 401


Lambda     K      H
   0.325    0.142    0.407 

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: 526
Number of extensions: 28
Number of successful extensions: 4
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: 419
Length of database: 401
Length adjustment: 31
Effective length of query: 388
Effective length of database: 370
Effective search space:   143560
Effective search space used:   143560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 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