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_RS26955 BWI76_RS26955 MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Koxy:BWI76_RS26955
          Length = 426

 Score =  612 bits (1579), Expect = e-180
 Identities = 293/412 (71%), Positives = 342/412 (83%), Gaps = 1/412 (0%)

Query: 7   APRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQ 66
           A +RWWYIMPIVFITYSLAYLDRAN+ FA+A+G+ +DL IT  +SSLLGALFFLGYFFFQ
Sbjct: 7   ATKRWWYIMPIVFITYSLAYLDRANFSFASAAGITEDLGITKGISSLLGALFFLGYFFFQ 66

Query: 67  VPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIY 126
           +PGAIYAE+RSV+KLIF+ LILWG  A+LTGMV ++  L AIRF+LGVVEAAVMPAMLIY
Sbjct: 67  IPGAIYAERRSVRKLIFICLILWGACASLTGMVHNIPALAAIRFILGVVEAAVMPAMLIY 126

Query: 127 LCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVLWAFIWW 186
           + +WFT++ERSRANTFLILGNPVT+LWMSVVSGYL++ F WR MFIIEG+PAV+WAF WW
Sbjct: 127 ISNWFTKSERSRANTFLILGNPVTVLWMSVVSGYLIQAFGWREMFIIEGVPAVIWAFCWW 186

Query: 187 RLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSIG 246
            LV D+P Q +WL   EK AL+E L  EQQGIKPV+NY EAFRS  V++L +QYF WSIG
Sbjct: 187 VLVKDKPSQVNWLAESEKAALQEQLEREQQGIKPVRNYGEAFRSRNVVLLCMQYFAWSIG 246

Query: 247 VYGFVLWLPSILKQAAA-LDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPL 305
           VYGFVLWLPSI++     + +V  GWLS+VPYL A +AM+ VSWASD+MQ RK FVWP L
Sbjct: 247 VYGFVLWLPSIIRSGGENMGMVEVGWLSSVPYLAATIAMIVVSWASDKMQNRKLFVWPLL 306

Query: 306 LIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALIN 365
           LIAA AF GS+ +G  HFW SYTLLVIAGA MYAPYGPFFAI+PE+LP NVAGGAMALIN
Sbjct: 307 LIAAFAFIGSWAVGANHFWVSYTLLVIAGAAMYAPYGPFFAIIPEMLPRNVAGGAMALIN 366

Query: 366 SMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQAR 417
           SMGALGSF GSW VGYLNG TG P ASY+FM  AL V+V LT ++ P+   +
Sbjct: 367 SMGALGSFFGSWFVGYLNGTTGSPSASYIFMGVALFVSVWLTLIVKPANNQK 418


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: 828
Number of extensions: 39
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: 425
Length of database: 426
Length adjustment: 32
Effective length of query: 393
Effective length of database: 394
Effective search space:   154842
Effective search space used:   154842
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