GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Sinorhizobium meliloti 1021

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate SMc00094 SMc00094 betaine aldehyde dehydrogenase

Query= BRENDA::P49189
         (494 letters)



>FitnessBrowser__Smeli:SMc00094
          Length = 487

 Score =  456 bits (1172), Expect = e-132
 Identities = 241/474 (50%), Positives = 321/474 (67%), Gaps = 7/474 (1%)

Query: 24  DASGTE-KAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAAR 82
           DA+GT  ++  PATG +IA    +    V  A+  AK A   W+  S   R RIL  AA 
Sbjct: 18  DAAGTVIESIYPATGEIIARLHAATPGIVEKAIAAAKRAQPEWAAMSPTARGRILKRAAE 77

Query: 83  IIREREDEIATMECINNGKSIFEARL-DIDISWQCLEYYAGLA-ASMAGEHIQLPGGSFG 140
           ++R+R  E++ +E ++ GK I E  + D        E++ G+A A++ G++I L GG F 
Sbjct: 78  LMRQRNRELSELETLDTGKPIQETIVADPTSGADSFEFFGGVAPAALNGDYIPL-GGDFA 136

Query: 141 YTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAG 200
           YT+R PLGVCVGIGAWNYP QIA WK APAL  GNAMVFKPS  TP+ AL +AEI  EAG
Sbjct: 137 YTKRVPLGVCVGIGAWNYPQQIACWKGAPALVAGNAMVFKPSENTPLGALKIAEILIEAG 196

Query: 201 VPPGLFNVVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSP 260
           +P GLFNV+QG  ATG  L  HPDVAKVS TGSVPTG K+   +A  +K VT+ELGGKSP
Sbjct: 197 LPKGLFNVIQGDRATGPLLVNHPDVAKVSLTGSVPTGKKVAGAAAAELKHVTMELGGKSP 256

Query: 261 LIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDP 320
           LI+F D D+ +A+ GA++ NF + GQVC NGTRVFVQ++I + F   + ++T+ I IGDP
Sbjct: 257 LIVFDDADLESAIGGAMLGNFYSTGQVCSNGTRVFVQRKIKEPFLARLKERTEAIVIGDP 316

Query: 321 LLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLTN 380
           L E T++GP+++    ++V  ++   K +GA+++ GG I  P +    +G Y++P V  +
Sbjct: 317 LDEATQLGPMVSAAQRDKVFSYIGKGKAEGARLVTGGGI--PNNVS-GEGTYIQPTVFAD 373

Query: 381 CRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQA 440
             D MT  +EEIFGPVM +L FD E EV+ RAN T FGL+AGVFT D+ RAHRV   L+A
Sbjct: 374 VTDGMTIAREEIFGPVMCVLDFDDEVEVIARANATEFGLSAGVFTADLTRAHRVADRLEA 433

Query: 441 GTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494
           GT +IN YN+ PVE+PFGG K+SGFGREN    + +Y++LKTV V MG VE+ +
Sbjct: 434 GTLWINTYNLCPVEIPFGGSKQSGFGRENSVAALNHYTELKTVYVGMGPVEAPY 487


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: 651
Number of extensions: 34
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: 494
Length of database: 487
Length adjustment: 34
Effective length of query: 460
Effective length of database: 453
Effective search space:   208380
Effective search space used:   208380
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