GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA 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)



>lcl|FitnessBrowser__Phaeo:GFF501 PGA1_c05130 aldehyde dehydrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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