GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuP in Klebsiella michiganensis M5al

Align Putrescine importer PuuP (characterized)
to candidate BWI76_RS03640 BWI76_RS03640 amino acid permease-associated protein

Query= SwissProt::P76037
         (461 letters)



>FitnessBrowser__Koxy:BWI76_RS03640
          Length = 447

 Score =  245 bits (625), Expect = 2e-69
 Identities = 142/439 (32%), Positives = 251/439 (57%), Gaps = 22/439 (5%)

Query: 15  KTRLRKSLKLWQVVMMGLAYLTPMTVFDTFGIVSGISDGHVPASYLLALAGVLFTAISYG 74
           K  L ++L    +++ G+ ++ P+  F  FG V   + G V  +YL+ +  + FTA+SY 
Sbjct: 9   KQELHRALTFRDLLVYGMIFMVPIAPFGVFGYVWDGAQGMVALAYLIGMVAMFFTAMSYW 68

Query: 75  KLVRQFPEAGSAYTYAQKSINPHVGFMVGWSSLLDYLFLPMINVLLAKIYLSALFPEVPP 134
            + R FP +GS Y YAQ+ I+P VGF  GW  LLDY+ +P +  +++   L+ + P VP 
Sbjct: 69  SMSRAFPVSGSVYAYAQRGIHPIVGFFAGWLILLDYILVPSLLYIVSAAALAPMLPGVPG 128

Query: 135 WVWVVTFVAILTAANLKSVNLVANFNTLFVLVQISIMVVFIFLVVQGLHKGEGVGTVWSL 194
           W+W+V F+AI +  NL+ +   A  N   ++ +I ++ VF+ L +  L+ G G G + +L
Sbjct: 129 WLWIVGFIAINSLINLRGITFTARANNTILIAEIVVLSVFVVLGLIALYSGAGAGHL-TL 187

Query: 195 QPFISENAHLIPIITGA-TIVCFSFLGFDAVTTLSEETPDAARVIPKAIFLTAVYGGVIF 253
            P  + +   +P++ GA +I   SFLGFD ++TLSEET D    + KA       G ++ 
Sbjct: 188 DPLYNADKFSLPLVMGAVSIAVLSFLGFDGISTLSEETKDGVDTVGKASL-----GALML 242

Query: 254 IAASFFMQLFF-PDISR---FKDPDAALPEIALYVGGKLFQSIFLCTTFVN-TLASGLAS 308
           + + F +Q +   D+++   F   D A  + A   GG   + + + +T ++  +A+ L +
Sbjct: 243 VGSLFILQTWIAADLAQGMTFSSLDTAFYDTANLAGGGWLKYVTMWSTVISWGIANALVA 302

Query: 309 HASVSRLLYVMGRDNVFPERVFGYVHPKWRTPALNVIMVGIVAL-SALFF--DLVTATAL 365
            A+VSR+L+ M RD   P+ +   VHP+ +TP ++ + V +++L S L+F  D+   + L
Sbjct: 303 QAAVSRILFAMARDKQLPQ-LLAKVHPRLKTPYVSTLFVALISLASGLWFYGDIDNLSRL 361

Query: 366 INFGALVAFTFVNLSVFNHFWRRKGMNKSWKDHFHYLLMPLVGALTVGVLWVNLESTSLT 425
           +NFGAL+ F  ++++V N++  R+   KS ++   +LL P+VG   +G +   +++ +  
Sbjct: 362 VNFGALMGFLVLHIAVINYYIIRQ---KS-RNLVVHLLFPVVGLCIIGFVIYEMDAQAKV 417

Query: 426 LGLVWASLGGAYLWYLIRR 444
           LGL W ++G  Y  YL+ R
Sbjct: 418 LGLSWLAVGVVY--YLLMR 434


Lambda     K      H
   0.328    0.141    0.437 

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: 613
Number of extensions: 32
Number of successful extensions: 6
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: 461
Length of database: 447
Length adjustment: 33
Effective length of query: 428
Effective length of database: 414
Effective search space:   177192
Effective search space used:   177192
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 (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