GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylT in Klebsiella michiganensis M5al

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter

Query= SwissProt::P0AE24
         (472 letters)



>FitnessBrowser__Koxy:BWI76_RS24055
          Length = 464

 Score =  594 bits (1532), Expect = e-174
 Identities = 298/456 (65%), Positives = 366/456 (80%), Gaps = 3/456 (0%)

Query: 16  RDTRRMNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEWVVSSMMLGAAIG 75
           R  + M  FV   AA+AGLLFGLDIGVIAGALPFI + F +++  QEWVVSSMM GAA+G
Sbjct: 9   RSNKTMTFFVCFLAALAGLLFGLDIGVIAGALPFIANEFQISAHTQEWVVSSMMFGAAVG 68

Query: 76  ALFNGWLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLGIAVGIASYTAPL 135
           A+ +GWLSF+LGRK SLM GAILFV GS+ SA A +VE+L+ +RV+LG+AVG+ASYTAPL
Sbjct: 69  AVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVGVASYTAPL 128

Query: 136 YLSEMASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAMLGVLALPAVLLIILV 195
           YLSE+A E +RG MISMYQLM+T+GI+ A+LSDTAFSYSG WR MLGV+ +PAVLL+I V
Sbjct: 129 YLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYSGAWRWMLGVIIIPAVLLLIGV 188

Query: 196 VFLPNSPRWLAEKGRHIEAEEVLRMLRDTSEKAREELNEIRESLKLKQGGWALFKINRNV 255
           VFLP+SPRW A K R ++AE VL  LRDTS +A+ EL+EIRESLK+KQ GW+LFK N N 
Sbjct: 189 VFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLKVKQSGWSLFKENSNF 248

Query: 256 RRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVVGLTFMFATFIAV 315
           RRAVFLG+LLQ MQQFTGMN+IMYYAP+IF++AG+  T +QM  T++VGLT + ATFIA+
Sbjct: 249 RRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTEQMWGTVIVGLTNVLATFIAI 308

Query: 316 FTVDKAGRKPALKIGFSVMALGTLVLGYCLMQFDNGTASSGLSWLSVGMTMMCIAGYAMS 375
             VD+ GRKP L +GF VMALG  +LG        G  S+   + +V M +M I G+AMS
Sbjct: 309 GLVDRWGRKPTLILGFIVMALGMGILG---SMMHIGIHSATAQYFAVLMLLMFIVGFAMS 365

Query: 376 AAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIGAAGTFWLYTALN 435
           A P++W+LCSEIQPLK RDFGITCST TNW++NMI+GATFLT+L+S+G+A TFW+Y  LN
Sbjct: 366 AGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNSLGSANTFWVYGGLN 425

Query: 436 IAFVGITFWLIPETKNVTLEHIERKLMAGEKLRNIG 471
           I F+ +T WLIPETKNV+LEHIER LM G KLR IG
Sbjct: 426 ILFIFLTLWLIPETKNVSLEHIERNLMKGRKLREIG 461


Lambda     K      H
   0.327    0.138    0.409 

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: 768
Number of extensions: 40
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: 472
Length of database: 464
Length adjustment: 33
Effective length of query: 439
Effective length of database: 431
Effective search space:   189209
Effective search space used:   189209
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