GapMind for catabolism of small carbon sources

 

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

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_02464 H281DRAFT_02464 betaine aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Burk376:H281DRAFT_02464
          Length = 489

 Score =  256 bits (653), Expect = 2e-72
 Identities = 164/482 (34%), Positives = 249/482 (51%), Gaps = 9/482 (1%)

Query: 1   MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60
           MA     + YI G +V++   +  D V+PA  E L  V  ++  D+D A Q+A E  + W
Sbjct: 1   MAVFATQRLYIGGTYVDATGGETFDTVDPANGETLATVQQASSADVDRAVQSAREGQREW 60

Query: 61  SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALG-EVGRGIENVEFAAGAP 119
           + +   +R+RIL     +L +  +ELA L T + GK   E    ++  G + +E+ AG  
Sbjct: 61  AALTGMQRSRILRRAVDILRERNDELAALETRDTGKPIAETQAVDIVTGADVIEYYAGLA 120

Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179
           + + G  +    T       R P+GV  GI  +N+P+ + CW    A+A GN  I KPSE
Sbjct: 121 TAIEGQQIPLRPTSFVYTR-REPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSE 179

Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYK- 238
            TPL   KL E++ +AG+P GVFNVV G   V   +  HP+I+ ISF G    G+ V   
Sbjct: 180 VTPLSALKLAEIYTEAGVPPGVFNVVQGDGRVGAMLAAHPDIEKISFTGGVETGKKVMSM 239

Query: 239 KGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIAD 298
            G+ +LK V    G K+  +V +DANLE      + A F S+G+ C     V V+  + +
Sbjct: 240 AGASSLKEVTMELGGKSPLLVFDDANLERAADIAMSANFFSSGQVCTNGTRVFVQRSVLE 299

Query: 299 EFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGR---E 355
            F A + E+V  I++G   D     GP++     ++ L YI+ G++EGARL+  G+   E
Sbjct: 300 RFEALVLERVKRIRVGAPGDASTNFGPLVSAAQLQKVLGYIDSGVQEGARLIAGGKRLSE 359

Query: 356 NVSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLF 415
                G +V PT+F     +M I ++EIF PV+S++   N  EAIE AN++ +   A + 
Sbjct: 360 GHFGQGQYVEPTVFTGCHDDMRIVREEIFGPVMSILIFDNEDEAIERANRTAYGLAAGVV 419

Query: 416 TSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475
           T N          ++AG+  IN    +P A  P  G+K S  G    NG  +++ YTR K
Sbjct: 420 TENLARAHRVIHRLEAGICWINTWGESP-AEMPVGGYKQS--GVGRENGITTLEHYTRIK 476

Query: 476 VV 477
            V
Sbjct: 477 SV 478


Lambda     K      H
   0.318    0.136    0.396 

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: 534
Number of extensions: 25
Number of successful extensions: 4
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: 487
Length of database: 489
Length adjustment: 34
Effective length of query: 453
Effective length of database: 455
Effective search space:   206115
Effective search space used:   206115
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: 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