GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putP in Pseudomonas stutzeri RCH2

Align L-proline uptake porter, PutP (characterized)
to candidate GFF3020 Psest_3078 sodium/proline symporter

Query= TCDB::Q9I5F5
         (506 letters)



>lcl|FitnessBrowser__psRCH2:GFF3020 Psest_3078 sodium/proline
           symporter
          Length = 494

 Score =  762 bits (1968), Expect = 0.0
 Identities = 375/492 (76%), Positives = 431/492 (87%), Gaps = 1/492 (0%)

Query: 1   MSVNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWL 60
           MS++TPTLITF+IYIAAM+LIG  AYR+T NF DYILGGRSLGSFVTALSAGASDMSGWL
Sbjct: 1   MSISTPTLITFLIYIAAMILIGFVAYRATKNFDDYILGGRSLGSFVTALSAGASDMSGWL 60

Query: 61  LMGLPGAVYLSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFED 120
           LMGLPGA++++GLSESWIAIGLIVGA+LNWLFVAGRLRV TEHN NALTLPDYF++RFED
Sbjct: 61  LMGLPGAIFVAGLSESWIAIGLIVGAWLNWLFVAGRLRVHTEHNHNALTLPDYFSHRFED 120

Query: 121 NSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGF 180
            SR+LRIFSALVILVFFTIYCASG+VAGARLFES+FG+ YE ALW GAAATI Y FIGGF
Sbjct: 121 ESRMLRIFSALVILVFFTIYCASGVVAGARLFESSFGVPYEYALWIGAAATILYVFIGGF 180

Query: 181 LAVSWTDTVQASLMIFALILTPVIVMLATGGVEPTFTAIELKDATSFDMLKGASFIGVIS 240
           LAVSWTDTVQA+LMIFAL++TPV V+LA G +      I  ++  +FDM  G SF+ +IS
Sbjct: 181 LAVSWTDTVQATLMIFALLITPVFVILALGDMGAAMDTIATQNPAAFDMFSGLSFVAIIS 240

Query: 241 LMAWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFFGIAYFQAHP 300
           L+AWGLGYFGQPHIL RFMAADS+K+IP ARRI M WMIL L GAVAVGFFGIAYF  HP
Sbjct: 241 LLAWGLGYFGQPHILVRFMAADSIKTIPNARRIGMAWMILTLAGAVAVGFFGIAYFAGHP 300

Query: 301 EQAGAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKA 360
           EQAGAVS+N ERVF+EL KILFNPW+AG++LS +LAAVMSTLS QLLV SSALT+DFYKA
Sbjct: 301 EQAGAVSQNGERVFMELVKILFNPWVAGIILSGVLAAVMSTLSAQLLVSSSALTQDFYKA 360

Query: 361 FLRKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVSYAWAGFGAAFGPLVLFSL 420
            LRK ASQ ELVWVGR MVLL+A+IAI +ASNPE++VLGLVSYAWAGFGAAFGP+VL SL
Sbjct: 361 MLRKSASQTELVWVGRGMVLLIALIAIGIASNPESKVLGLVSYAWAGFGAAFGPVVLISL 420

Query: 421 LWKRMTRNGALAGMIVGAATVILWKNLLGWTGLYEIIPGFLFASVAIVVFSLLGKAPSTS 480
           LWKRMTRNGALAGM+VGA TV++WK  +G  GLYEIIPGF+ AS+AI V S +G  P+ S
Sbjct: 421 LWKRMTRNGALAGMLVGAVTVVVWKEFIG-LGLYEIIPGFILASIAIFVVSKMGAEPAPS 479

Query: 481 MLKRFDDAEQEY 492
           ++KRF++A+ +Y
Sbjct: 480 IIKRFEEADADY 491


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: 1027
Number of extensions: 48
Number of successful extensions: 2
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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