GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Pseudomonas fluorescens FW300-N2E3

Align L-proline uptake porter, PutP (characterized)
to candidate AO353_12815 AO353_12815 proline:sodium symporter PutP

Query= TCDB::Q9I5F5
         (506 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12815
          Length = 494

 Score =  802 bits (2072), Expect = 0.0
 Identities = 412/494 (83%), Positives = 449/494 (90%), Gaps = 6/494 (1%)

Query: 1   MSVNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWL 60
           MS + PTLITFVIYIAAMVLIG  AYRSTNN SDYILGGRSLGS VTALSAGASDMSGWL
Sbjct: 1   MSASNPTLITFVIYIAAMVLIGFMAYRSTNNLSDYILGGRSLGSVVTALSAGASDMSGWL 60

Query: 61  LMGLPGAVYLSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFED 120
           LMGLPGA+Y+SGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNG+ALTLPDYF++RFED
Sbjct: 61  LMGLPGAIYMSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGDALTLPDYFSSRFED 120

Query: 121 NSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGF 180
            S LLRI SA+VILVFFTIYCASGIVAGARLFESTFG+SYETALWAGAAATIAYTF+GGF
Sbjct: 121 KSGLLRIISAVVILVFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATIAYTFVGGF 180

Query: 181 LAVSWTDTVQASLMIFALILTPVIVMLATGGVEPTFTAIELKDATSFDMLKGASFIGVIS 240
           LAVSWTDTVQA+LMIFAL+LTP+IV+LATGG++ TF AIE +D  +FDMLK  SFIG+IS
Sbjct: 181 LAVSWTDTVQATLMIFALLLTPIIVLLATGGIDTTFLAIEAQDPGNFDMLKNTSFIGIIS 240

Query: 241 LMAWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFFGIAYFQAHP 300
           LM WGLGYFGQPHILARFMAADSVKSI  ARRISMTWMILCLGG VAVGFFGIAYF A+P
Sbjct: 241 LMGWGLGYFGQPHILARFMAADSVKSIANARRISMTWMILCLGGTVAVGFFGIAYFSANP 300

Query: 301 EQAGAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKA 360
             A  VSEN ERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYK+
Sbjct: 301 AVAMPVSENHERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKS 360

Query: 361 FLRKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVSYAWAGFGAAFGPLVLFSL 420
           FLRK ASQ+ELVWVGRAMVL VA+IAI LA+NPENRVLGLVSYAWAGFGAAFGP+VL S+
Sbjct: 361 FLRKNASQVELVWVGRAMVLAVALIAIALAANPENRVLGLVSYAWAGFGAAFGPVVLISV 420

Query: 421 LWKRMTRNGALAGMIVGAATVILWK--NLLGWTGLYEIIPGFLFASVAIVVFSLLGKAPS 478
           LWK MTRNGALAG++VGA TVI+WK  NLL   GLYEIIPGF+FAS+AI++ S +G  PS
Sbjct: 421 LWKGMTRNGALAGIVVGALTVIVWKHFNLL---GLYEIIPGFIFASLAILLVSKMG-VPS 476

Query: 479 TSMLKRFDDAEQEY 492
             ML+RF  AE+++
Sbjct: 477 AGMLQRFAAAEKDF 490


Lambda     K      H
   0.326    0.138    0.421 

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: 966
Number of extensions: 35
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: 506
Length of database: 494
Length adjustment: 34
Effective length of query: 472
Effective length of database: 460
Effective search space:   217120
Effective search space used:   217120
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: 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