GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_04205 in Pseudomonas fluorescens FW300-N1B4

Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate Pf1N1B4_397 Hexuronate transporter

Query= reanno::WCS417:GFF828
         (454 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_397
          Length = 436

 Score =  401 bits (1031), Expect = e-116
 Identities = 189/431 (43%), Positives = 283/431 (65%), Gaps = 9/431 (2%)

Query: 6   PTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQI 65
           P+  R+ I+++LF+   INY DR+ ++IA  +L  DLGID + +G IFSAFGW Y A QI
Sbjct: 15  PSRKRFFIMVLLFITVVINYLDRSNLSIAAPALTSDLGIDPIHVGLIFSAFGWTYAAMQI 74

Query: 66  PGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFP 125
           PGGWL+DR   + +Y++++  WSL TV+ G+   F      +ALF+LR  VG  EAP++P
Sbjct: 75  PGGWLVDRVPPRILYSVALLLWSLATVMLGFAASF------IALFVLRMAVGALEAPAYP 128

Query: 126 GNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIF 185
            N+R+V  WFP  ER TA   + S Q+       P++ W+ + +GW  VF+  G +GII+
Sbjct: 129 INSRVVTTWFPERERATAIGFYTSGQFVGLAFLTPVLAWLQHQYGWHMVFVSTGAVGIIW 188

Query: 186 SLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRM 245
           ++IW  V   PR     N+AE   I   G +VD+  +  K K      W  +  +L+ R 
Sbjct: 189 AVIWYAVYREPRDFKGANDAEIELIREGGGLVDIQAEAAKTKAKFS--WIDLGIVLSKRK 246

Query: 246 MLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISD 305
           + G+YLGQ+C+N   +FFLTWFP YLV+ RGM  +K+G +ASLP +  F+G +  G  SD
Sbjct: 247 LWGIYLGQFCLNSTLWFFLTWFPTYLVKYRGMDFIKSGLLASLPFLAAFVGVLCSGFFSD 306

Query: 306 YLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAVV 365
           +L+R+G+++ FARK PIIGGLLIS+SI+  N+V+   +V+ F+ALAFFG G+ ++ W++V
Sbjct: 307 FLIRRGYTVGFARKLPIIGGLLISTSIIGANFVESTPLVIAFLALAFFGNGLASITWSLV 366

Query: 366 SDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYL 425
           S  +P ++ GL+GG+FN  GNLA+ITTPIVIG++ S   SF  A+ ++   AL+   SY+
Sbjct: 367 STLAPARLLGLTGGVFNFIGNLAAITTPIVIGFLAS-GDSFAPAITYISVLALLGALSYV 425

Query: 426 VIVGPIKRVVL 436
           ++VG ++R+ L
Sbjct: 426 LLVGKVERIKL 436


Lambda     K      H
   0.327    0.142    0.444 

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: 653
Number of extensions: 29
Number of successful extensions: 4
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: 454
Length of database: 436
Length adjustment: 32
Effective length of query: 422
Effective length of database: 404
Effective search space:   170488
Effective search space used:   170488
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: 51 (24.3 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