GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Burkholderia phytofirmans PsJN

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BPHYT_RS16075 BPHYT_RS16075 D-arabinitol 4-dehydrogenase

Query= BRENDA::O08355
         (493 letters)



>FitnessBrowser__BFirm:BPHYT_RS16075
          Length = 470

 Score =  245 bits (626), Expect = 2e-69
 Identities = 153/446 (34%), Positives = 226/446 (50%), Gaps = 9/446 (2%)

Query: 29  IAHIGVGGFHRAHQAYYTDALMNT---GEGLDWSICGVGLRSEDRKARDDLAGQDYLFTL 85
           I HIG G FHRAHQA+Y   L      GE   WS+    +RS+     + LA Q+ ++TL
Sbjct: 14  ILHIGAGSFHRAHQAWYLHRLNEAKVAGEP-HWSLTVGNIRSDMNAVLEALAAQNGVYTL 72

Query: 86  YELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEF 145
             +    +     I SI  ++   +S  ALI+  A P  +I++ T+TEGGY +D+ + E 
Sbjct: 73  ETVTPQGERAYETIRSIERVVPWTESLDALIEAGADPACKIIAFTVTEGGYYLDEQD-EL 131

Query: 146 MAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLA 205
               P +  DL       T++G + A L  R  AG    T+ +CDNL  NG      +  
Sbjct: 132 DTANPDLAADLE--GGHTTIYGALAAILDARMKAGAGPVTLQTCDNLRSNGERFHAGMSE 189

Query: 206 FAALHNA-ELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQW 264
           F     A EL  W   + + P++MVDRITP  +   R ++    G+DDA PV+ E F+QW
Sbjct: 190 FLERRGASELAQWFDDNTASPSSMVDRITPRPTPDVRERVKAATGVDDAVPVMGEAFIQW 249

Query: 265 VLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMND 324
           V+ED F+ GRPAWEKVG +  D V PYEE KI +LN +H  + + G L G  ++HE   D
Sbjct: 250 VIEDNFIAGRPAWEKVGAELVDSVMPYEEAKIRILNATHSCIAWAGTLVGLNYIHEGTLD 309

Query: 325 PLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPK 384
                +   Y+  DV P L P P +DL  Y+  +++RFSN  I D  +RV +DG SK P 
Sbjct: 310 ADINKFAYEYVTEDVIPCLTPSP-LDLERYRDVVLERFSNPYIQDTNQRVAADGFSKLPG 368

Query: 385 FTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALI 444
           F  PT++     G      A++ A +  +L   +   + YT  D   +        +A  
Sbjct: 369 FIAPTLSECFERGVTPAATAMLPALFFRFLDRWNAGKLPYTYQDGVMDERVARAFFEAPD 428

Query: 445 SQRLLAVEEIFGTAIPNSPEFVAAFE 470
             +  A + +   ++  +PE  +A E
Sbjct: 429 PLKAFAADRLLWGSMAQTPELESALE 454


Lambda     K      H
   0.321    0.137    0.414 

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: 595
Number of extensions: 31
Number of successful extensions: 5
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: 493
Length of database: 470
Length adjustment: 34
Effective length of query: 459
Effective length of database: 436
Effective search space:   200124
Effective search space used:   200124
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: 52 (24.6 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