GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC in Klebsiella michiganensis M5al

Align Nucleoside permease NupC; Nucleoside-transport system protein NupC (characterized)
to candidate BWI76_RS20540 BWI76_RS20540 NupC/NupG family nucleoside CNT transporter

Query= SwissProt::P0AFF2
         (400 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS20540 BWI76_RS20540 NupC/NupG
           family nucleoside CNT transporter
          Length = 400

 Score =  725 bits (1872), Expect = 0.0
 Identities = 373/400 (93%), Positives = 395/400 (98%)

Query: 1   MDRVLHFVLALAVVAILALLVSSDRKKIRIRYVIQLLVIEVLLAWFFLNSDVGLGFVKGF 60
           MDRVLHF+LA+ VVAILALLVS +RK+IRIRYVIQLLVIEVLLAWFFLNSD+GLGFVKGF
Sbjct: 1   MDRVLHFILAIVVVAILALLVSHNRKQIRIRYVIQLLVIEVLLAWFFLNSDIGLGFVKGF 60

Query: 61  SEMFEKLLGFANEGTNFVFGSMNDQGLAFFFLKVLCPIVFISALIGILQHIRVLPVIIRA 120
           SEMFEKLLGFANEGTNFVFG+MND+GLAFFFLKVLCPIVFISALIGILQHIR+LP++IRA
Sbjct: 61  SEMFEKLLGFANEGTNFVFGNMNDKGLAFFFLKVLCPIVFISALIGILQHIRILPIVIRA 120

Query: 121 IGFLLSKVNGMGKLESFNAVSSLILGQSENFIAYKDILGKISRNRMYTMAATAMSTVSMS 180
           IG +LSK+NGMGKLESFNAVSSLILGQSENFIAYKDILGK+SRNRMYTMAATAMSTVSMS
Sbjct: 121 IGTVLSKINGMGKLESFNAVSSLILGQSENFIAYKDILGKMSRNRMYTMAATAMSTVSMS 180

Query: 181 IVGAYMTMLEPKYVVAALVLNMFSTFIVLSLINPYRVDASEENIQMSNLHEGQSFFEMLG 240
           IVGAYMTML+PKYVVAALVLNMFSTFIVLSLINPYRVD SEEN+QMSNLHEGQSFFEMLG
Sbjct: 181 IVGAYMTMLQPKYVVAALVLNMFSTFIVLSLINPYRVDESEENLQMSNLHEGQSFFEMLG 240

Query: 241 EYILAGFKVAIIVAAMLIGFIALIAALNALFATVTGWFGYSISFQGILGYIFYPIAWVMG 300
           EYILAGFKVAIIVAAMLIGFIALI+ALNALFATVTGWFGYSISFQGILGYIFYP+AWVMG
Sbjct: 241 EYILAGFKVAIIVAAMLIGFIALISALNALFATVTGWFGYSISFQGILGYIFYPVAWVMG 300

Query: 301 VPSSEALQVGSIMATKLVSNEFVAMMDLQKIASTLSPRAEGIISVFLVSFANFSSIGIIA 360
           VP+ EALQVGSIMATKLVSNEFVAMMDLQK+A+TLSPRAEGIIS+FLVSFANFSSIGIIA
Sbjct: 301 VPAGEALQVGSIMATKLVSNEFVAMMDLQKVAATLSPRAEGIISIFLVSFANFSSIGIIA 360

Query: 361 GAVKGLNEEQGNVVSRFGLKLVYGSTLVSVLSASIAALVL 400
           GA+KGLNEEQGNVVSRFGLKLVYGSTLVSVLSASIAALVL
Sbjct: 361 GAIKGLNEEQGNVVSRFGLKLVYGSTLVSVLSASIAALVL 400


Lambda     K      H
   0.328    0.141    0.393 

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: 668
Number of extensions: 17
Number of successful extensions: 1
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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