GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Phaeobacter inhibens BS107

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate GFF1302 PGA1_c13180 ABC transporter, ATP binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>FitnessBrowser__Phaeo:GFF1302
          Length = 334

 Score =  349 bits (896), Expect = e-101
 Identities = 189/357 (52%), Positives = 241/357 (67%), Gaps = 25/357 (7%)

Query: 1   MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60
           M +++L  V K++G +EVI  +DL I+ GEF VFVGPSGCGKSTLLR+IAGLE+I+SG +
Sbjct: 1   MGQIKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTI 60

Query: 61  TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120
            ID     ++ P+KRG+AMVFQSYALYPHM+VR+N+ F ++ AG+P  E ++R++ AA  
Sbjct: 61  RIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAA 120

Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180
           L L   LDR+P QLSGGQRQRVAIGRAIVR P  FLFDEPLSNLDA LRV MR+EI+ LH
Sbjct: 121 LNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH 180

Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240
           K+LATT++YVTHDQVEAMT+ADKIVV++AGV+EQVGSP++LY  P N+FVAGFIGSPKMN
Sbjct: 181 KRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMN 240

Query: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAALDL-AID 299
            L G                         QAA   A TIGIRPEH   +    +    I 
Sbjct: 241 LLTGP------------------------QAAQHNAATIGIRPEHLSISETEGMWAGTIG 276

Query: 300 MLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRL 356
           + EHLG +TF + +     + + V       L  G+R+    D   +  F  +G R+
Sbjct: 277 VSEHLGSDTFFHVQCDAFDDPLTVRASGELDLGYGERVFLTPDMTHLHRFGSDGLRI 333


Lambda     K      H
   0.321    0.139    0.396 

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: 395
Number of extensions: 18
Number of successful extensions: 3
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: 358
Length of database: 334
Length adjustment: 29
Effective length of query: 329
Effective length of database: 305
Effective search space:   100345
Effective search space used:   100345
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: 49 (23.5 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