GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3020
          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 (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