GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galP in Klebsiella michiganensis M5al

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

Query= SwissProt::P96710
         (464 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS21205 BWI76_RS21205 MFS
           transporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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