GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupC in Sphingobium czechense LL01

Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate WP_066605839.1 V473_RS13315 nucleoside transporter

Query= uniprot:A0KU05
         (419 letters)



>NCBI__GCF_001046645.1:WP_066605839.1
          Length = 440

 Score =  409 bits (1052), Expect = e-119
 Identities = 214/454 (47%), Positives = 306/454 (67%), Gaps = 49/454 (10%)

Query: 1   MNILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVS 60
           M++L+ L G++++LAI F LS++++AI  R VG A  +QA     VLYVP G+ I+  +S
Sbjct: 1   MHLLIGLAGILLILAIAFALSSDRRAIRPRVVGAAFLLQAGIAILVLYVPAGRAIIGGMS 60

Query: 61  DAVSSVIGYAQNGIGFLFGDLANFKLGFI-FAVNVLPVIVFFSSLIAVLYYLGIMQWIIR 119
             V++++ YAQ G  F+FG LA  ++G   FA+  LPVI+FF+SL+++LYYLGIMQ+I+R
Sbjct: 61  RGVANLLSYAQAGTDFIFGPLAKPEIGGASFAIAALPVIIFFASLVSILYYLGIMQFIVR 120

Query: 120 IIGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAG 179
            +GG ++   G S+ ES+ A ANIFVGQ+E+PLV+RP++  +T  +LFA+M  G+A +AG
Sbjct: 121 WVGGAIEWVTGVSKVESLCAAANIFVGQSESPLVIRPYLAGLTPPQLFAVMTSGMAGVAG 180

Query: 180 SVLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMH---------------------PETE 218
           ++LA YA MG+ I+YL+AASFMAAPGGLLMAK+M                      PET 
Sbjct: 181 TILAAYASMGIKIDYLLAASFMAAPGGLLMAKIMMPDPRAPVQGELPLGDHPDLLLPETR 240

Query: 219 VA-------------KNDMDELPEDPDKPANVLDAAAAGASSGMHLALNVGAMLLAFVGL 265
           ++                M +   D +KPAN++ AAA GA +G+ LA+ VGAM+LAFV L
Sbjct: 241 ISGAGPAALLPEGTPGEPMPQASHDEEKPANLIMAAAQGAQTGVKLAVAVGAMVLAFVAL 300

Query: 266 IAMINGIIGGVGGWFGVEGLTLELILGYIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEF 325
           +A+ NGI+GG+G WFG   L+ +++LGY+F P+ +L+ +PW EA VAG   G K+V+NEF
Sbjct: 301 VALANGILGGIGAWFGYPTLSFQMLLGYVFQPVMYLLNIPWAEAQVAGGLFGTKVVLNEF 360

Query: 326 VAYLNFAPYLKDIADGGMIVADTGLAMTDRTKAIISFALCGFANLSSIAILLGGLGAMAP 385
           VAY+N           G +      A++  T AII+FALCGFAN SSIAI +   G +AP
Sbjct: 361 VAYINL----------GQVQG----ALSPATIAIITFALCGFANFSSIAIQMAVTGNLAP 406

Query: 386 NRRHDLAKLGIRAVIAGSLANLMSATIAGLFLAI 419
           N+R  +AKLG++A++AGSLANLMSA +AGL L++
Sbjct: 407 NQRPMIAKLGLKALVAGSLANLMSAALAGLMLSL 440


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: 634
Number of extensions: 34
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: 440
Length adjustment: 32
Effective length of query: 387
Effective length of database: 408
Effective search space:   157896
Effective search space used:   157896
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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