GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Phaeobacter inhibens BS107

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase

Query= BRENDA::Q97UA1
         (478 letters)



>FitnessBrowser__Phaeo:GFF501
          Length = 476

 Score =  327 bits (837), Expect = 7e-94
 Identities = 179/457 (39%), Positives = 262/457 (57%), Gaps = 5/457 (1%)

Query: 21  DINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQ 80
           +INP+D   VL        +D++ AI  A      W+ +   +R  +L   G  +     
Sbjct: 20  NINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTPQQRFDVLDAIGTEILARKA 79

Query: 81  EFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLG 140
           E   L++ EEGKTL + + E  R+  + KF+     + +G+ L S  P   +   + P+G
Sbjct: 80  ELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGEILGSVRPGVGVEVTRSPVG 139

Query: 141 VVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNL 200
           VV LITPWNFP++IP WK+APALA G+  V+KPA  TP     L E+++++GLPEGV N+
Sbjct: 140 VVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCAHALAEIINRSGLPEGVFNI 199

Query: 201 VVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDK 260
           V G GS VG T+V   ++ A+SFTGS E G  I    G + +  ++QLE+GGKN + V  
Sbjct: 200 VFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAACGAQRK--KLQLEMGGKNPMVVLD 257

Query: 261 SADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPGTED-V 319
            ADL  A + ++ G F  TGQ CTA+SRLI+ + ++ +F   L ER+   RVG   +D  
Sbjct: 258 DADLETAVDASLNGAFFSTGQRCTASSRLIVTEGIHDRFVAALGERMTGLRVGNALDDST 317

Query: 320 DMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPG-KGYFLEPTIFEGVTSDMRLFKE 378
            +GPVVDE Q +KDL Y++   + G +++ G  +    KG++L P +    ++DMR+ +E
Sbjct: 318 QIGPVVDERQLEKDLYYLDVAASEGGQVLGGQTLQRSTKGFYLAPALVTETSNDMRINQE 377

Query: 379 EIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTV 438
           E+FGP+ SV    D DEA+ + N   +G +AGI    +K    F +  EAG+  VN PT 
Sbjct: 378 EVFGPLASVIRVADYDEALVVANDTPFGLSAGICTGSLKYATHFKAHAEAGMAMVNLPTA 437

Query: 439 GLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475
           G++   PFGG K S     +E G  A EFY K KT Y
Sbjct: 438 GVDYHVPFGGTKGSSFGA-REQGSHAKEFYTKVKTAY 473


Lambda     K      H
   0.316    0.135    0.389 

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: 34
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: 478
Length of database: 476
Length adjustment: 33
Effective length of query: 445
Effective length of database: 443
Effective search space:   197135
Effective search space used:   197135
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 (21.6 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