GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Frischella perrara PEB0191

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_039103680.1 FPB0191_RS02210 amino acid permease

Query= SwissProt::A0A0H2VDI7
         (470 letters)



>NCBI__GCF_000807275.1:WP_039103680.1
          Length = 484

 Score =  257 bits (656), Expect = 7e-73
 Identities = 145/398 (36%), Positives = 230/398 (57%), Gaps = 20/398 (5%)

Query: 16  EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPS-IIFVYMIIGFMLFFVMRAM 74
           +  L+R+L  RH+ +IAIGG+IGTGLF+ SG TI+ AGP+  +  Y IIG M++F+M ++
Sbjct: 2   QNKLKRDLKARHLTMIAIGGSIGTGLFVASGATIAQAGPAGSLLSYAIIGVMVYFLMTSL 61

Query: 75  GELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFP-GL 133
           GEL        +F+ + S  +    G+  GW YW+ W +T   D+VA      +WF  G 
Sbjct: 62  GELAAYLPVSGTFATYGSKYVDESFGFAIGWNYWYNWAITVAVDLVAAQLVISYWFDFGA 121

Query: 134 SDWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVA--MHFQSPT 191
             W+ SL  ++++  LN+ +VK FGE EFWF++IK++ +V  I VGL+M+   +H  S T
Sbjct: 122 YSWLWSLLFLVIIFFLNVISVKGFGEAEFWFSLIKVITVVVFIAVGLLMIVGILHGGSDT 181

Query: 192 GVEASFAHLWNDGGW-FPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAIN 250
            +     H WN G   F  G S       I  F+F G EL+G  A E+KDPEK++P+++ 
Sbjct: 182 AIGW---HNWNIGDAPFVGGFSSMIGVAMIVGFSFQGTELIGIAAGESKDPEKNIPKSMR 238

Query: 251 SIPIRIIMFYVFSLIVIMSVTPWSS--------VVPEKSPFVELFVLVGLPAAASVINFV 302
            +  RI++FY+F++ VI  + P++              SPF  +F   GL +AA+++N V
Sbjct: 239 QVFWRILLFYIFAIFVISLIIPYTDPRLLRNDEADISVSPFTLVFEHAGLLSAAAIMNAV 298

Query: 303 VLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGL-TFSCICLLGGVVM 361
           VLTS  S+ NSG+++++RML+ LA+EG APK F +LSK  +P   L   + + +L  +  
Sbjct: 299 VLTSVLSAGNSGLYASTRMLYALAKEGKAPKIFGRLSKSGIPTMSLIATTIVAMLCFLTS 358

Query: 362 LYVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYRK 399
           ++ +  V   +  +  +S +     W  I  S+  +RK
Sbjct: 359 MFKDQQV---YLWLLNLSGMTGFIAWLGIAISHYRFRK 393


Lambda     K      H
   0.329    0.141    0.441 

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: 629
Number of extensions: 43
Number of successful extensions: 6
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: 470
Length of database: 484
Length adjustment: 33
Effective length of query: 437
Effective length of database: 451
Effective search space:   197087
Effective search space used:   197087
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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