GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Thermoactinomyces daqus H-18

Align General amino-acid permease GAP2 (characterized)
to candidate WP_033101984.1 JG50_RS0115245 amino acid permease

Query= SwissProt::A0A1D8PK89
         (588 letters)



>NCBI__GCF_000763315.1:WP_033101984.1
          Length = 484

 Score =  381 bits (978), Expect = e-110
 Identities = 199/479 (41%), Positives = 301/479 (62%), Gaps = 9/479 (1%)

Query: 77  LTRSLKNRHLQMIAIGGSIGTGLFVGSGSSLHTGGPAGLLIAYILIGTMIYCTVMSLGEL 136
           L R LK RHL MIAIGGSIGTG+F+ SG+S+   GP G L+AY+ IG M+Y  + SLGE+
Sbjct: 10  LKRGLKARHLSMIAIGGSIGTGVFLASGASISEAGPGGALVAYLAIGIMVYFLMTSLGEM 69

Query: 137 AVTFPVSGAFVTYNSRFIDPSWGFAMAWNYAMQWLVVLPLELVAAAMTVKYWDAKTNSAA 196
           A   PV+G+F TY  RF+DP+ GFAM WNY   W + + +EL A ++ + YW   + S  
Sbjct: 70  ATFMPVAGSFSTYAGRFVDPALGFAMGWNYWYNWAITIAVELSAGSLIMDYWFPHSPSIL 129

Query: 197 FVVIFYVLIVAINFFGVRGYGEAEFIFSAVKVLAVLGFIILGIVLCAG--GGPQGGYIGG 254
           +  +F +L+  +N   V+GYGE+E+ FS +KV  V+ FI++G+++  G  GG     IG 
Sbjct: 130 WSALFLLLMFGLNALSVKGYGESEYWFSFIKVATVIIFIVIGLLMIFGIMGGEA---IGF 186

Query: 255 KNWYIEGAPFPNGAKGVITVFVNAAFAFAGTELCGLAAAETENPRKSLPKACKQVFWRIT 314
           KN+ I  APF +G  G+++VF+ A F+F GTEL G+AA E+ENPRK++PKA +QVFWRI 
Sbjct: 187 KNFTINDAPFHHGWLGILSVFMIAGFSFQGTELVGVAAGESENPRKNVPKAIRQVFWRIL 246

Query: 315 LFYVICLTLVGLLVPWNDERLLGSSSADASASPFVISIRNAGIKGLPSVMNVVIMIAVLS 374
           LFY + + ++GL++P+ +  L+G      + SPF I    AG+    SVMN VI+ +VLS
Sbjct: 247 LFYALAILVMGLVLPYTNPNLVGGDVNQIAKSPFTIIFEKAGLAFAASVMNAVILTSVLS 306

Query: 375 VGNSSVYGSSRTLAALAASNQAPKIFGYIDKQGRPLVGIIAQLLVGLLCFLAASDKQGEV 434
            GNS +Y S+R L  +A   +APK+F  ++++G P+  ++    VG + FLA+   QG++
Sbjct: 307 AGNSGMYASTRMLWQMAKEGKAPKLFAKVNRRGVPVFALLLTTAVGAVAFLASLVGQGKI 366

Query: 435 FNWLLALSGLSSIFTWGSINVCLIRFRRALAAQGRDTGELVFTSQVGVIGAIWGAFLNTV 494
           + WLL  SGLS    W  I +   RFRRA  AQGRD   LV+ ++    G ++   L  +
Sbjct: 367 YIWLLNASGLSGFIAWLGIAISHYRFRRAYVAQGRDLNHLVYRAKWFPFGPLFALVLCVI 426

Query: 495 VLCLQFWIAVWPLHSSPSAEAFFSAYLTVPVVIVFYVGHKLWTKNWQVYICAKDIDIDT 553
           V+  Q + A     ++        +Y+ +P+ I+ ++G+K W K  +V I  K++D+++
Sbjct: 427 VIVGQNYQAF--TGNTIDWNGILVSYIGLPLFILLWLGYK-WVKKTKV-IPLKEVDLES 481


Lambda     K      H
   0.324    0.139    0.431 

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: 815
Number of extensions: 39
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: 588
Length of database: 484
Length adjustment: 35
Effective length of query: 553
Effective length of database: 449
Effective search space:   248297
Effective search space used:   248297
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 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