GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Phaeobacter inhibens BS107

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Phaeo:GFF501
          Length = 476

 Score =  269 bits (687), Expect = 2e-76
 Identities = 160/470 (34%), Positives = 245/470 (52%), Gaps = 5/470 (1%)

Query: 8   KNYINGEWVESKTDQYEDVVNPA-TKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVP 66
           KN I G+W  S+T      +NP+ T++VL     S  ED++ A   A +A   W+     
Sbjct: 4   KNLIAGDW--SETVAAAANINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTPQ 61

Query: 67  RRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDS 126
           +R  +L      +   K EL  L++ E GK   E +GE  R  +  +F AG      G+ 
Sbjct: 62  QRFDVLDAIGTEILARKAELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGEI 121

Query: 127 LASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTE 186
           L S+   V     R P+GVVG I P+NFP+ +P W    A+A G+  +LKP+E TP    
Sbjct: 122 LGSVRPGVGVEVTRSPVGVVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCAH 181

Query: 187 KLVELFEKAGLPKGVFNVVYGAHDVVNGIL-EHPEIKAISFVGSKPVGEYVYKKGSENLK 245
            L E+  ++GLP+GVFN+V+G    V   L +   + AISF GS   G  +        K
Sbjct: 182 ALAEIINRSGLPEGVFNIVFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAACGAQRK 241

Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQ 305
           ++Q   G KN  +VL+DA+LE  V   +  AF S G+RC A + + V EGI D F+A L 
Sbjct: 242 KLQLEMGGKNPMVVLDDADLETAVDASLNGAFFSTGQRCTASSRLIVTEGIHDRFVAALG 301

Query: 306 EKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVG 365
           E++  +++GN LDD   +GPV+ E   ++ L Y++    EG +++       S  G+++ 
Sbjct: 302 ERMTGLRVGNALDDSTQIGPVVDERQLEKDLYYLDVAASEGGQVLGGQTLQRSTKGFYLA 361

Query: 366 PTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYF 425
           P +    + +M I ++E+F P+ SVIRV +  EA+ +AN + F   A + T +     +F
Sbjct: 362 PALVTETSNDMRINQEEVFGPLASVIRVADYDEALVVANDTPFGLSAGICTGSLKYATHF 421

Query: 426 RENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475
           + + +AGM  +NL         PF G K S FG     G  + +FYT+ K
Sbjct: 422 KAHAEAGMAMVNLPTAGVDYHVPFGGTKGSSFGA-REQGSHAKEFYTKVK 470


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: 526
Number of extensions: 27
Number of successful extensions: 2
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: 476
Length adjustment: 34
Effective length of query: 453
Effective length of database: 442
Effective search space:   200226
Effective search space used:   200226
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