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 GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Phaeo:GFF2135
          Length = 485

 Score =  275 bits (702), Expect = 3e-78
 Identities = 161/476 (33%), Positives = 255/476 (53%), Gaps = 7/476 (1%)

Query: 6   KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65
           K  ++INGE+VE        V+  AT E +  V  +T   ++ A  TA  A K W+++  
Sbjct: 8   KASHFINGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKAWARMTG 67

Query: 66  PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMG 124
             R RIL     ++ +   +L+ L T + GK  +E L  +   G + +E+  G  + + G
Sbjct: 68  TERGRILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTG 127

Query: 125 DSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLL 184
           + +      V     R  +G+  GI  +N+P  + CW    A+A GN+ + KPSE TPL 
Sbjct: 128 EHIPLGEDWVYTK--REALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLC 185

Query: 185 TEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENL 244
             K+ E+  +AG P GVFNVV G  +V   ++  P +  +S  GS P G+ VY   +E +
Sbjct: 186 ALKVAEILIEAGAPAGVFNVVQGMGEVGGALVTDPRVDKVSLTGSVPTGKKVYAAAAEGM 245

Query: 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304
           K V    G K+  I+ +DA++++ V   +   F S+G+ C     V V++GI ++F+A+L
Sbjct: 246 KHVTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARL 305

Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFV 364
            E+  +  +G+ +D+    GP++ E+     L YIEKG EEGARL+C GR     DGYF+
Sbjct: 306 AERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGR-RADMDGYFI 364

Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424
            PT+F +VT +MTI ++EIF PV+SV+     +E +  AN +EF   A +FT +      
Sbjct: 365 EPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAHR 424

Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTAR 480
              N++AG   IN    AP+   PF G K+S  G    N K+++  +++ K V  R
Sbjct: 425 VIGNLEAGSCFINSYNDAPVE-APFGGVKAS--GVGRENSKEAIKHFSQVKSVYVR 477


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: 600
Number of extensions: 36
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: 487
Length of database: 485
Length adjustment: 34
Effective length of query: 453
Effective length of database: 451
Effective search space:   204303
Effective search space used:   204303
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