GapMind for catabolism of small carbon sources

 

Alignments for a candidate for exuT in Paraburkholderia bryophila 376MFSha3.1

Align Phthalate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate H281DRAFT_05311 H281DRAFT_05311 MFS transporter, ACS family, hexuronate transporter

Query= uniprot:D8IX31
         (418 letters)



>FitnessBrowser__Burk376:H281DRAFT_05311
          Length = 432

 Score =  635 bits (1639), Expect = 0.0
 Identities = 298/410 (72%), Positives = 356/410 (86%), Gaps = 2/410 (0%)

Query: 4   VRGIRWYMVTLVTLALIVNYLARNTLSVAAPTMMKELDMSTQQYSYIVVAWQICYAVMQP 63
           ++GIRW+MV+LV   LI+NYLARNTLSVAAPT+MK+L ++T+QY+++VVAWQ+CYA MQP
Sbjct: 3   IKGIRWWMVSLVAAGLIINYLARNTLSVAAPTLMKDLHITTEQYAHVVVAWQLCYAFMQP 62

Query: 64  VAGYILDAVGTKIGFGIFALAWSLVCAAAAFATGWQSLAFFRALLGITEAAGIPGGVKAS 123
           VAG++LD VGTKIGF  FALAWSL CAAAA++TGW+SLAFFR LLGI EAAGIP GVKA+
Sbjct: 63  VAGFLLDTVGTKIGFAAFALAWSLACAAAAWSTGWRSLAFFRGLLGIAEAAGIPAGVKAT 122

Query: 124 TEWFPAKERSVAIGWFNIGSSIGALCAPPLVVWTILHGGWKMSFVVVGALGVIWFVLWML 183
           +EWFPAKERSVAIGWFNIGSSIGAL APPLVVW +LHG W+++FV+VG  G+IW V+WM+
Sbjct: 123 SEWFPAKERSVAIGWFNIGSSIGALLAPPLVVWALLHGQWQLAFVIVGVAGIIWSVVWMV 182

Query: 184 FYKSPRDQKLLSPEERAYILEGQE--KSPEKVQRESWTKIVRSRNFWSIAIPRFLSEPAW 241
            YK PR+QKLL   ER YIL GQE   S     + SW+ ++RSR+FW+I IPR LSEPAW
Sbjct: 183 LYKHPRNQKLLGDGERDYILSGQEAKHSDAGAPKRSWSAMLRSRDFWAIGIPRILSEPAW 242

Query: 242 QTFNAWIPLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSPLFHKHLKVSLFTSRK 301
           QTFNAWIPLYM TERHMN+KEIA++AW+PFLAADIGCVLGGYLSPLFHK+ KVSLFTSRK
Sbjct: 243 QTFNAWIPLYMMTERHMNLKEIALYAWMPFLAADIGCVLGGYLSPLFHKYAKVSLFTSRK 302

Query: 302 LVMLVGSLSMIGPACVGFVDSPYVAIALLSIGGFAHQTLSGALYSITSDVFTKNQVATAT 361
           +V +VG+L MIGPACVG V SPYVA+ALL +GGFAHQTLSGALY+ITSD+F KN+VATAT
Sbjct: 303 MVFVVGALCMIGPACVGLVASPYVAVALLCVGGFAHQTLSGALYAITSDMFGKNEVATAT 362

Query: 362 GLTGMSGYLGATLFTLLFGILVTQIGYGPLFVLLAAFDLVAVAVVFAIAR 411
           G+ GM+GYLGA  FT LFG+LVTQ+GY PLFV+LA FD++A AVV  +A+
Sbjct: 363 GMGGMAGYLGAAAFTALFGVLVTQVGYSPLFVVLAVFDIIAAAVVCLLAK 412


Lambda     K      H
   0.327    0.138    0.440 

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: 792
Number of extensions: 28
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 418
Length of database: 432
Length adjustment: 32
Effective length of query: 386
Effective length of database: 400
Effective search space:   154400
Effective search space used:   154400
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