GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__MR1:203375 SO4296 NupC family protein (NCBI ptt
           file)
          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 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, 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