GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putP in Klebsiella michiganensis M5al

Align Osmoregulated proline transporter OpuE; Osmoprotectant uptake; Proline uptake system (characterized)
to candidate BWI76_RS25550 BWI76_RS25550 sodium:pantothenate symporter

Query= SwissProt::O06493
         (492 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS25550 BWI76_RS25550
           sodium:pantothenate symporter
          Length = 483

 Score =  187 bits (476), Expect = 5e-52
 Identities = 141/484 (29%), Positives = 242/484 (50%), Gaps = 38/484 (7%)

Query: 1   MSIEIIISLGIYFIAMLLIGWYAFKKTTD---INDYMLGGRGLGPFVTALSAGAADMSGW 57
           M  EII+ L +Y + +  +  YA +K +    +++Y LG R +G FV A++  A  +S  
Sbjct: 1   MQFEIIVVLLVYLLVVFGLSIYAMRKRSSGSFLSEYFLGSRSMGGFVLAMTLTATYISAS 60

Query: 58  MLMGVPGAMFATGLS----------TLWLALGLTIGAYSNYLLLAPRLRAYTEAADDAIT 107
             +G PGA +  GL           T+WL+LG+ +G    + +LA R         +AIT
Sbjct: 61  SFIGGPGAAYKYGLGWVLLAMIQVPTIWLSLGI-LG--KKFAILARRY--------NAIT 109

Query: 108 IPDFFDKRFQHSSSLLKIVSALIIMIFFTLYTSSGMVSGGRLFESAFGADYKLGLFLTTA 167
           + D    R+Q  S  +  ++++ +++ F    +   + G RL E+A G  Y+ GL +   
Sbjct: 110 LNDMLQARYQ--SRAVVWIASVSLLVAFVGAIAVQFIGGARLLETAAGIKYETGLLIFGI 167

Query: 168 VVVLYTLFGGFLAVSLTDFVQGAIMFAALVLVPIVAFTHVGGVAPTFHEIDAVNPHLLDI 227
            + LYT FGGF A  L D +QG +M    +++ +      GG+      +  ++P L+  
Sbjct: 168 TIALYTAFGGFRASVLNDTMQGMVMLIGTIVLLVGVVHAAGGLHNAVDTLQHIDPKLVSP 227

Query: 228 FKGASVISIISYLA--WGL---GYYGQPHIIVRFMAIKDIKDLKPARRIGMSWMIITVLG 282
             GA+ I   +++   W L   G  G PH  VR ++ KD K +     IG   + I + G
Sbjct: 228 -HGANDILTPAFMTSFWVLVCFGVIGLPHTAVRCISYKDSKAVHRGIIIGTIVVAILMFG 286

Query: 283 SVLTGLIGVAYAHKFGVAVKDPEMIFIIFSKILFHPLITGFLLSAILAAIMSSISSQLLV 342
             L G +G A      V    P+ +       +  P   G  L+A +AAIMS++++ LL 
Sbjct: 287 MHLAGALGRAVLPHLTV----PDQVIPTLMVQVLPPWAAGLFLAAPMAAIMSNVNAHLLQ 342

Query: 343 TASAVTEDLYRSFF-RRKASDKELVMIGRLSVLVIAVIAVLLSLNPNSTILDLVGYAWAG 401
            ++ + +DL+ S    +K ++++L  I  ++ LV+ ++ +L +  P   I+ L   A+ G
Sbjct: 343 ASATIIKDLWLSAQPTKKHNEQKLKRISTIATLVLGILMMLAAWRPPEMIIWLNLLAFGG 402

Query: 402 FGSAFGPAILLSLYWKRMNEWGALAAMIVGAATVLIWITTGLAKSTGVYEIIPGFILSMI 461
             + F   ++L LYW+R N  GAL+AMIVG     I  T  L +  G + I+P  +LS++
Sbjct: 403 LEAVFLWPLVLGLYWERANATGALSAMIVGGVLYAILATFNL-QYLGFHPIVPSLLLSLL 461

Query: 462 AGII 465
           A ++
Sbjct: 462 AFLV 465


Lambda     K      H
   0.328    0.142    0.421 

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: 645
Number of extensions: 33
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: 492
Length of database: 483
Length adjustment: 34
Effective length of query: 458
Effective length of database: 449
Effective search space:   205642
Effective search space used:   205642
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 (21.8 bits)
S2: 52 (24.6 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