GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Pseudomonas putida KT2440

Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate PP_4946 PP_4946 sodium/L-proline transporter

Query= SwissProt::P07117
         (502 letters)



>FitnessBrowser__Putida:PP_4946
          Length = 542

 Score =  759 bits (1960), Expect = 0.0
 Identities = 378/491 (76%), Positives = 426/491 (86%), Gaps = 1/491 (0%)

Query: 3   ISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWLLM 62
           +  P+ +TF +YI  M+LIGF A+R+T N  DYILGGRSLG  VTALSAGASDMSGWLLM
Sbjct: 51  MGNPLTITFVIYIAAMVLIGFAAYRATNNLSDYILGGRSLGSVVTALSAGASDMSGWLLM 110

Query: 63  GLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKS 122
           GLPGA++ +G+SE+WIAIGLT+GA++NW  VAGRLRV TE+N +ALTLPDYF+ RFED S
Sbjct: 111 GLPGAIYFAGLSEAWIAIGLTVGAYLNWLFVAGRLRVQTEHNGDALTLPDYFSSRFEDNS 170

Query: 123 RILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLA 182
            +LRIISA+VIL+FFTIYCASGIVAGARLFESTFGMSYETALWAGAAATI YTF+GGFLA
Sbjct: 171 GLLRIISAIVILVFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATIAYTFVGGFLA 230

Query: 183 VSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIISLM 242
           VSWTDTVQASLMIFALILTPVIV+IS GGF  +   I+  +  N DMLKG  F+ IISLM
Sbjct: 231 VSWTDTVQASLMIFALILTPVIVLISTGGFDQTFAAIEAVNPANFDMLKGATFIGIISLM 290

Query: 243 GWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPAL 302
           GWGLGYFGQPHILARFMAADS  SI  ARRISMTWMILCLAG  AVGFFGIAYF+ HP L
Sbjct: 291 GWGLGYFGQPHILARFMAADSVKSIAKARRISMTWMILCLAGTCAVGFFGIAYFSAHPEL 350

Query: 303 AGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKAFL 362
           AG V++N ERVFIELA+ILFNPW+AG+LLSAILAAVMSTLSCQLLVCSSA+TED YKAFL
Sbjct: 351 AGPVSENHERVFIELAKILFNPWVAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKAFL 410

Query: 363 RKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSVMW 422
           RK+ASQ ELVWVGR+MVL VAL+AIA+AANPENRVLGLV+YAWAGFGAAFGPVVL SV+W
Sbjct: 411 RKNASQVELVWVGRLMVLAVALIAIAMAANPENRVLGLVAYAWAGFGAAFGPVVLISVLW 470

Query: 423 SRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAMQK 482
             MTRNGALAG+++GALTVI+WK F  LGLYEIIPGF+F SI IV+ S LG +PS  M K
Sbjct: 471 KGMTRNGALAGIVVGALTVILWKNFDTLGLYEIIPGFLFASIAIVLVSKLG-SPSQTMVK 529

Query: 483 RFAEADAHYHS 493
           RF  ADA YH+
Sbjct: 530 RFEAADAAYHA 540


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: 948
Number of extensions: 50
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 502
Length of database: 542
Length adjustment: 35
Effective length of query: 467
Effective length of database: 507
Effective search space:   236769
Effective search space used:   236769
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 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