GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araE in Klebsiella michiganensis M5al

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate BWI76_RS21205 BWI76_RS21205 MFS transporter

Query= SwissProt::P96710
         (464 letters)



>FitnessBrowser__Koxy:BWI76_RS21205
          Length = 478

 Score =  292 bits (747), Expect = 2e-83
 Identities = 161/452 (35%), Positives = 261/452 (57%), Gaps = 12/452 (2%)

Query: 20  MGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLS-PFMEGLVISSIMIGGVVGVG 78
           MG+V  I   A  GGLL+GYD  VI GA  F +  +S++ P   G  +SS ++G V G  
Sbjct: 10  MGYVWTICLVAACGGLLFGYDWVVIGGAKPFYEAWFSITDPAQSGWAMSSALVGCVFGAL 69

Query: 79  ISGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYI 138
           ISG+ +D+ GR+  L+ +A+LF+ SA  +A++      ++ RI+GG+GIG+ S+LS  YI
Sbjct: 70  ISGWCADKLGRKLPLILSAVLFSASAWGTAVASSFDMFVVYRIVGGVGIGLASALSPLYI 129

Query: 139 TEAAPPAIRGSLSSLYQLFTILGISATYFINL---------AVQRSGTYEWGVHTGWRWM 189
            E +P   RG   ++ QL  ++G+ A   INL         A Q+     W    GWRWM
Sbjct: 130 AEVSPAEKRGRFVAVNQLTIVIGVLAAQLINLMIAEPVATGATQQMIVETWNGQMGWRWM 189

Query: 190 LAYGMVPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSL-K 248
               +VP++ F +++  VPESPRWL KAGK   A   L RI     A   L++I ++L K
Sbjct: 190 FGAELVPALAFLVLMFFVPESPRWLMKAGKPERARAALERIGSADYADRILRDIAHTLEK 249

Query: 249 IEQMGSLSQLFKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTC 308
                S   L  P ++  ++IG++LA+F Q  G+N I  Y  EIF   GF  N+   +  
Sbjct: 250 DNHKVSYGALLAPQVKPIVIIGMVLAVFQQWCGINVIFNYAQEIFASAGFDINSTLKSIV 309

Query: 309 IVGVVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILG 368
             GVV ++FT+ A+ L+DK+GR+KLM +G++ + +  +LI  ++   +  G  +++L+L 
Sbjct: 310 ATGVVNLVFTLAALPLVDKIGRRKLMLLGASGLTLIYVLIAGAYAMGI-MGWPVLLLVLA 368

Query: 369 FVAAFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYT 428
            +A + +++ P+TW++++EIFPN +R  A  + T+ LW A + +    P++    G A +
Sbjct: 369 AIAIYALTLAPVTWVLLAEIFPNRVRGLAMSLGTLALWIACFLLTYTFPLLNAGLGAAGS 428

Query: 429 FWIFAVINILCFLFVVTICPETKNKSLEEIEK 460
           F ++ VI    +L+++   PETK  +LE +E+
Sbjct: 429 FLLYGVICAAGYLYILRNVPETKGVTLEALEE 460


Lambda     K      H
   0.327    0.142    0.425 

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: 550
Number of extensions: 25
Number of successful extensions: 5
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: 464
Length of database: 478
Length adjustment: 33
Effective length of query: 431
Effective length of database: 445
Effective search space:   191795
Effective search space used:   191795
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