GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Klebsiella michiganensis M5al

Align KguT (characterized, see rationale)
to candidate BWI76_RS12915 BWI76_RS12915 4-hydroxyphenylacetate permease

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Koxy:BWI76_RS12915
          Length = 457

 Score =  210 bits (534), Expect = 8e-59
 Identities = 128/412 (31%), Positives = 214/412 (51%), Gaps = 18/412 (4%)

Query: 14  IMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIYA 73
           ++  +F+ +  ++LDR N GFA  + M+ DL +T  +  L   LF++ Y  F VP  I  
Sbjct: 28  LVAFLFVLFVFSFLDRINIGFAGLT-MSQDLGLTSTMFGLAATLFYVTYVLFGVPSNIML 86

Query: 74  EKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFTR 133
            +   ++ I V +++WG  +T T    S   L A+R ++GV EA  +P +L+YL  WF  
Sbjct: 87  SRVGARRWIAVIMVVWGVASTCTLFATSAGTLYALRMIVGVAEAGFVPGILLYLTWWFPS 146

Query: 134 AERSRANTFLILGNPVTILWMSVVSGYL------VKHFDWRWMFIIEGLPAVLWAFIWWR 187
             R+RAN   ++  P+T+++ S++SGY+      +    W+W+F++EGLP+V+   + W 
Sbjct: 147 WYRARANALFMIAMPLTMMFGSMLSGYILALDGVMNLRGWQWLFLLEGLPSVILGVVTWF 206

Query: 188 LVDDRPEQASWLKAQEKTALREALAAEQQ------GIKPVKNYREAFRSPKVIILSLQYF 241
            +DD+P  A WL A EK  L+  + +++         +PV  +RE F +P V++  L YF
Sbjct: 207 YLDDKPADAKWLNADEKQTLQRMMESDRSVNRKMLTRRPVSLWREVF-TPVVVLYILAYF 265

Query: 242 CWSIGVYGFVLWLPSILKQ-AAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRF 300
           C +  +    +W P ILK   A+   +T G L+A+P    ++ M+  S  SDR+++RKR 
Sbjct: 266 CLTNSLSAINIWTPQILKSFNASSSNITVGLLAAIPQFCTIVVMMWWSKRSDRLKERKRH 325

Query: 301 VWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGA 360
              P L +A  +  + +  T H     + L++A A  +     F+      +        
Sbjct: 326 TIYPYLFSAAGWLLTSL--TAHPLIQLSGLIMASAGAFTAMTLFWTTPDRAISVGAQAVV 383

Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNP 412
           +A I+  G +GS     L+G ++ +TG   A   FM G LLV  AL  V  P
Sbjct: 384 LATISGAGNIGSGLSPLLIGVMHDMTGNFNAGLWFMAG-LLVIGALVLVYIP 434


Lambda     K      H
   0.328    0.140    0.457 

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: 597
Number of extensions: 39
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: 425
Length of database: 457
Length adjustment: 32
Effective length of query: 393
Effective length of database: 425
Effective search space:   167025
Effective search space used:   167025
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: 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