GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proY in Klebsiella michiganensis M5al

Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate BWI76_RS19685 BWI76_RS19685 lysine transporter

Query= SwissProt::P46349
         (469 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS19685 BWI76_RS19685 lysine
           transporter
          Length = 489

 Score =  344 bits (882), Expect = 4e-99
 Identities = 174/387 (44%), Positives = 251/387 (64%), Gaps = 9/387 (2%)

Query: 7   GLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPG-AVVSYALAGLLVIFIMRMLGE 65
           GL++ELK RH+TMI+I G IG GLFV SG+ I   GPG A++SY L GL+V F+M  LGE
Sbjct: 12  GLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYILIGLMVYFLMTSLGE 71

Query: 66  MSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLW 125
           ++A  P SGSF+ Y  + +    GF +GW YW+ W + IA++ +A   ++ YWF D P W
Sbjct: 72  LAAFMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMTYWFPDAPGW 131

Query: 126 LTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFS 185
           + S +   ++ L N  SVK FGE EYWFSLIKV T+I F+IVG   IFG   G++P G+S
Sbjct: 132 VWSALFLGIMFLLNWISVKGFGEAEYWFSLIKVATVIIFIIVGVMMIFGIFKGAQPAGWS 191

Query: 186 NLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRIIV 245
           N       F  G ++++   ++V FSF GTE++ IAAGE+ NP +++ +A R V WRI++
Sbjct: 192 NWVIDDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESENPEKNIPRAVRQVFWRILL 251

Query: 246 FYVGSIAIVVALLPWNSANILE--------SPFVAVLEHIGVPAAAQIMNFIVLTAVLSC 297
           FYV +I I+  ++P+   ++L         SPF  V +H G+ +AA IMN ++LTAVLS 
Sbjct: 252 FYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAIMNAVILTAVLSA 311

Query: 298 LNSGLYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVF 357
            NSG+Y ++RMLY+LA   +APR F KLSK GVP  A+ A T  + +  + + F   TV+
Sbjct: 312 GNSGMYASTRMLYTLACDGKAPRIFSKLSKGGVPRNALYATTVIAGLCFLSSMFGNQTVY 371

Query: 358 LFLVNSSGAIALLVYLVIAVSQLKMRK 384
           L+L+N+SG    + +L IA+S  + R+
Sbjct: 372 LWLLNTSGMTGFIAWLGIAISHYRFRR 398


Lambda     K      H
   0.326    0.140    0.417 

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: 647
Number of extensions: 24
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: 469
Length of database: 489
Length adjustment: 34
Effective length of query: 435
Effective length of database: 455
Effective search space:   197925
Effective search space used:   197925
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: 51 (24.3 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, the preprint on GapMind for carbon sources, 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