GapMind for catabolism of small carbon sources

 

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

Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate Pf1N1B4_691 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= SwissProt::P9WQI3
         (393 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_691
          Length = 351

 Score =  254 bits (650), Expect = 2e-72
 Identities = 148/319 (46%), Positives = 198/319 (62%), Gaps = 16/319 (5%)

Query: 1   MAEIVLDHVNKSYPDGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGE 60
           M  ++L++V K Y     AV+D+NL + +G+ +  +GPSGCGKTT L MIAGLE ++ GE
Sbjct: 1   MTGLILENVEKHYGSA-CAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGGE 59

Query: 61  LRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAK 120
           +R+ GE +       R+  MVFQS AL+PHMTV +NIA+PL L  + KAD   +V E  +
Sbjct: 60  IRLDGEDIGHTPAHQRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLE 119

Query: 121 ILDLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQL 180
           ++ L  ++DR  ++LSGGQRQRVA+ RAI   PK  L+DEPLS LDAKLR  M+ EI QL
Sbjct: 120 LIQLQEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALDAKLRESMQVEIRQL 179

Query: 181 QRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPAM 240
           Q+RL  TT+ VTHDQ EAMT+ D VVV+     QQ+G+P E+Y  PAN FVA FIGS   
Sbjct: 180 QQRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHPANEFVADFIGSG-- 237

Query: 241 NFFPARLTAIG---LTLPFGEVTLAPEVQGVIAAHPKPENVIVGVRPEHIQDAALIDAYQ 297
           N FPA  TA+G   ++LP G+    P    ++      E V + +RPE +Q    +   Q
Sbjct: 238 NIFPA--TALGNGKVSLPGGDALQVPICSSIVVG----EKVKMLIRPEDLQ----LSQPQ 287

Query: 298 RIRALTFQVKVNLVESLGA 316
                    KV  V  +GA
Sbjct: 288 ATAGNRLLGKVTFVRDIGA 306


Lambda     K      H
   0.319    0.135    0.377 

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: 344
Number of extensions: 13
Number of successful extensions: 1
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: 393
Length of database: 351
Length adjustment: 30
Effective length of query: 363
Effective length of database: 321
Effective search space:   116523
Effective search space used:   116523
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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