GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdaD in Pseudomonas fluorescens FW300-N2E2

Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate Pf6N2E2_862 Fumarylacetoacetate hydrolase family protein

Query= reanno::HerbieS:HSERO_RS19360
         (391 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_862
          Length = 392

 Score =  457 bits (1177), Expect = e-133
 Identities = 237/383 (61%), Positives = 283/383 (73%), Gaps = 4/383 (1%)

Query: 11  LPEDHAQATLIGRIWQPGV--GPVLVRIDADGAYDLTLIAATSSELLELDNPAAAVRSAT 68
           LP D    TLIGR W PG   GP  V +  +G +DL+   +T SELLE  +P   VR A 
Sbjct: 12  LPVDGLAGTLIGRAWIPGAIAGPSPVVLRDEGVFDLSETFSTISELLEHTSPLLVVRQAP 71

Query: 69  NMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVIEEQARGDA 128
               I T++ LL N  +   D  +  LL P DLQ +KA+GVTF +SM+ERVIEEQARGDA
Sbjct: 72  GRY-IGTVEALLGNTGSHA-DPGKASLLPPADLQVIKAAGVTFASSMIERVIEEQARGDA 129

Query: 129 GKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPDAEIFTKAQ 188
            KAESVR+ +   IGDNL ++ PGSPEA RLK VL+ QG+WSQYLEVGIGPDAEIFTKA 
Sbjct: 130 AKAESVRRLVHEAIGDNLRAIKPGSPEAMRLKAVLIKQGMWSQYLEVGIGPDAEIFTKAP 189

Query: 189 PMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEGRSALLLGK 248
            +++VG G E+GIH KS WNNPEPEIVLA+NSRG+V G TLGNDVNLRDFEGRSALLL K
Sbjct: 190 VLAAVGSGSEIGIHRKSEWNNPEPEIVLAVNSRGQVHGVTLGNDVNLRDFEGRSALLLSK 249

Query: 249 AKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMISRDPLQLV 308
           AKDNNASCA+GPFIRLFD  F++DDVR   + + V G +GF L+GSSSM++ISRDPL LV
Sbjct: 250 AKDNNASCAIGPFIRLFDEAFTLDDVRNCVVDLHVQGDDGFALEGSSSMALISRDPLDLV 309

Query: 309 EHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGALVNTVNFS 368
              +G +HQYPDG +LFLGT+FAPTQDR  PG GFTH+  D V+I +P LG L NTV +S
Sbjct: 310 AQTVGGDHQYPDGFMLFLGTLFAPTQDREEPGSGFTHKQGDEVSIGSPLLGTLRNTVTYS 369

Query: 369 DQTAPWTFGLTALFKNLADRKLI 391
            + APWTFGL A+  NLA R L+
Sbjct: 370 HEAAPWTFGLRAMMHNLAARGLL 392


Lambda     K      H
   0.317    0.134    0.387 

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: 476
Number of extensions: 14
Number of successful extensions: 3
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: 391
Length of database: 392
Length adjustment: 31
Effective length of query: 360
Effective length of database: 361
Effective search space:   129960
Effective search space used:   129960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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