GapMind for catabolism of small carbon sources

 

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

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate H281DRAFT_02464 H281DRAFT_02464 betaine aldehyde dehydrogenase

Query= BRENDA::P49189
         (494 letters)



>FitnessBrowser__Burk376:H281DRAFT_02464
          Length = 489

 Score =  489 bits (1258), Expect = e-142
 Identities = 248/483 (51%), Positives = 328/483 (67%), Gaps = 5/483 (1%)

Query: 14  YRGGARVEPADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMER 73
           Y GG  V+ A    T    +PA G  +AT   +   +V+ AVQ+A+   + W+  +GM+R
Sbjct: 10  YIGGTYVD-ATGGETFDTVDPANGETLATVQQASSADVDRAVQSAREGQREWAALTGMQR 68

Query: 74  CRILLEAARIIREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHI 132
            RIL  A  I+RER DE+A +E  + GK I E + +DI      +EYYAGLA ++ G+ I
Sbjct: 69  SRILRRAVDILRERNDELAALETRDTGKPIAETQAVDIVTGADVIEYYAGLATAIEGQQI 128

Query: 133 QLPGGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLL 192
            L   SF YTRREPLGVC GIGAWNYP QIA WKSAPALA GNAM+FKPS  TP+SAL L
Sbjct: 129 PLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEVTPLSALKL 188

Query: 193 AEIYSEAGVPPGLFNVVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMS-AKGIKPV 251
           AEIY+EAGVPPG+FNVVQG    G  L  HPD+ K+SFTG V TG K+M M+ A  +K V
Sbjct: 189 AEIYTEAGVPPGVFNVVQGDGRVGAMLAAHPDIEKISFTGGVETGKKVMSMAGASSLKEV 248

Query: 252 TLELGGKSPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQ 311
           T+ELGGKSPL++F D ++  A   A+ ANF + GQVC NGTRVFVQ+ +L++F   V+++
Sbjct: 249 TMELGGKSPLLVFDDANLERAADIAMSANFFSSGQVCTNGTRVFVQRSVLERFEALVLER 308

Query: 312 TQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGY 371
            +RI++G P    T  GPL++   L++VLG++    ++GA+++ GG      +     G 
Sbjct: 309 VKRIRVGAPGDASTNFGPLVSAAQLQKVLGYIDSGVQEGARLIAGGKRL--SEGHFGQGQ 366

Query: 372 YMRPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRA 431
           Y+ P V T C DDM  V+EEIFGPVMSIL FD E E +ERAN T +GLAAGV T ++ RA
Sbjct: 367 YVEPTVFTGCHDDMRIVREEIFGPVMSILIFDNEDEAIERANRTAYGLAAGVVTENLARA 426

Query: 432 HRVVAELQAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVE 491
           HRV+  L+AG C+IN +  SP E+P GGYK+SG GRENG  T+E+Y+++K+V VE+G  +
Sbjct: 427 HRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQVELGPYQ 486

Query: 492 SAF 494
             F
Sbjct: 487 PVF 489


Lambda     K      H
   0.320    0.137    0.411 

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: 687
Number of extensions: 31
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: 494
Length of database: 489
Length adjustment: 34
Effective length of query: 460
Effective length of database: 455
Effective search space:   209300
Effective search space used:   209300
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