GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Pseudomonas litoralis 2SM5

Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_090274945.1 BLU11_RS15570 sodium/proline symporter PutP

Query= SwissProt::P07117
         (502 letters)



>NCBI__GCF_900105005.1:WP_090274945.1
          Length = 500

 Score =  460 bits (1183), Expect = e-134
 Identities = 237/482 (49%), Positives = 325/482 (67%), Gaps = 18/482 (3%)

Query: 8   LVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWLLMGLPGA 67
           LV   +Y   M+ IG+ A+R T + DDY+L GR L P V ALSAGASDMSGWLLMGLPGA
Sbjct: 8   LVAIGLYFLTMLGIGYYAYRQTTDLDDYMLAGRKLSPGVAALSAGASDMSGWLLMGLPGA 67

Query: 68  VFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKSRILRI 127
           ++ SG+ E+WIAIGLT+GA++NW+ VA RLR +TE +NN++T+P +   RF+DK+R+LRI
Sbjct: 68  IYASGLVEAWIAIGLTIGAYLNWRFVAPRLRSYTEVSNNSITVPSFMENRFKDKTRLLRI 127

Query: 128 ISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLAVSWTD 187
            S ++IL+FFT Y +SG+VAG   FE++F   Y   +   +  T+ YT  GGFL  S TD
Sbjct: 128 ASGVIILVFFTFYVSSGMVAGGVFFEASFNTPYLFGMLLVSGITLTYTLFGGFLGASLTD 187

Query: 188 TVQASLMIFALILTPVIVIISVGGFGDSLEVIKQ-----------KSIENVDMLKGLNFV 236
            VQ  LM+ ALI+ PV+ +I +GG G++++ I               +    +L G + +
Sbjct: 188 VVQGLLMLAALIIVPVLTVIGMGGLGETIDAIHAADAAHNLANPGDELHRTSLLFGGSLL 247

Query: 237 AIISLMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYF 296
           AIIS   WGLGYFGQPHI+ RFMA  S       RRI + WMIL  +GAV  G  G+ YF
Sbjct: 248 AIISAASWGLGYFGQPHIIVRFMALRSSADAKAGRRIGIGWMILVASGAVFTGLIGVGYF 307

Query: 297 NDHPALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITED 356
           +     +  V  N E VF+ L+QILF+P +AG++L+A+LAA+MST+S QL+VCSSA+ ED
Sbjct: 308 H----TSNEVLDNPETVFLLLSQILFHPLVAGLVLAAVLAAIMSTVSSQLIVCSSALVED 363

Query: 357 LYKAFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVV 416
           LYK F  K  +  + V +GR+ VL VA++A  LA +P + +LGLV++AWAGFGAAFGP++
Sbjct: 364 LYKIF-GKDLTALQQVRLGRLGVLTVAVIAALLAIDPRSNILGLVAFAWAGFGAAFGPII 422

Query: 417 LFSVMWSRMTRNGALAGMIIGALTVIVWKQFGWLG--LYEIIPGFIFGSIGIVVFSLLGK 474
           L S+ W ++T  GALAGMI GA+ V +W     L   +YEI+PGF+  ++  +V SLL K
Sbjct: 423 LLSLFWRKLTAMGALAGMITGAVVVGIWGNIASLQALMYEIVPGFLACTVVAIVVSLLIK 482

Query: 475 AP 476
            P
Sbjct: 483 TP 484


Lambda     K      H
   0.328    0.140    0.436 

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: 747
Number of extensions: 51
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: 502
Length of database: 500
Length adjustment: 34
Effective length of query: 468
Effective length of database: 466
Effective search space:   218088
Effective search space used:   218088
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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