GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Paraburkholderia bryophila 376MFSha3.1

Align KguT (characterized, see rationale)
to candidate H281DRAFT_05212 H281DRAFT_05212 Sugar phosphate permease

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Burk376:H281DRAFT_05212
          Length = 429

 Score =  608 bits (1567), Expect = e-178
 Identities = 295/410 (71%), Positives = 336/410 (81%)

Query: 6   LAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFF 65
           LA RRWW IMPIVFITYSLAYLDRANYGFAAA+G+  DL I+  LSSL+GALFFLGYFFF
Sbjct: 5   LAIRRWWTIMPIVFITYSLAYLDRANYGFAAAAGINQDLGISKGLSSLIGALFFLGYFFF 64

Query: 66  QVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLI 125
           Q+PGAIYAE+RSVKKL+F SL+LWGG A LTGMV ++  L+ IRF+LGVVEAAVMPAMLI
Sbjct: 65  QIPGAIYAERRSVKKLVFWSLVLWGGCAALTGMVSNIPSLMVIRFVLGVVEAAVMPAMLI 124

Query: 126 YLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFIW 185
           ++ +WFT++ERSRANTFLILGNPVT+LWMSVVSGYLV  F WR MFI EG+PA+LWA  W
Sbjct: 125 FISNWFTKSERSRANTFLILGNPVTVLWMSVVSGYLVHSFGWRNMFIAEGIPAILWAVCW 184

Query: 186 WRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSI 245
           W +V D+P+Q SWL  Q+K  L + L AEQ  IKPV+NY EAFRS  VI L  QYFCWSI
Sbjct: 185 WFIVQDKPQQVSWLTQQQKDDLAQTLRAEQAAIKPVRNYSEAFRSSAVIKLCAQYFCWSI 244

Query: 246 GVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPL 305
           GVYGFVLWLPSILK  ++L +V  GWLSA+PYL A +AML  SWASD++ +RK FVWP L
Sbjct: 245 GVYGFVLWLPSILKNGSSLGMVETGWLSALPYLAATIAMLAASWASDKLNRRKVFVWPFL 304

Query: 306 LIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALIN 365
           LI A+AF  SY LG+ HFW SY  LVIAGA MYAPYGPFFAIVPELLP NVAGGAMALIN
Sbjct: 305 LIGAIAFAASYALGSTHFWLSYASLVIAGAAMYAPYGPFFAIVPELLPKNVAGGAMALIN 364

Query: 366 SMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQ 415
           SMGALGSF GS++VGYLNG TG P ASY FM  AL+ AV LT ++ P QQ
Sbjct: 365 SMGALGSFVGSYVVGYLNGATGSPAASYAFMSVALIAAVILTLIVKPQQQ 414


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: 806
Number of extensions: 35
Number of successful extensions: 1
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: 429
Length adjustment: 32
Effective length of query: 393
Effective length of database: 397
Effective search space:   156021
Effective search space used:   156021
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