GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Pedobacter sp. GW460-11-11-14-LB5

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  355 bits (912), Expect = e-102
 Identities = 200/477 (41%), Positives = 279/477 (58%), Gaps = 14/477 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           +I G++   V G  F+ +SP+DG+   K A     D   AV+ A   F +  WS+ +  +
Sbjct: 17  YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKT--WSKTSSTE 74

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L + A  +  N+E LA +ET+D GK + ++ + D+P       + A  I      +
Sbjct: 75  RSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSL 134

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
           +    + + L+  EP+GVV  I+PWNFPLLM  WKL PALA GN VVLKP+E +P++ + 
Sbjct: 135 SELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMV 194

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           + +L  +  +P GV+NV+ G+G  +G+AL  +  V    FTGST   + +M YA E N+ 
Sbjct: 195 LMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATE-NII 252

Query: 263 RIWLEAGGKSPNIVFA-----DAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317
            + LE GGKSPNI F+     D   L  A E A    A NQGE+CT  SRLL++  I +K
Sbjct: 253 PVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVM-FALNQGEICTCPSRLLIQEDIYEK 311

Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL-- 375
           F+  V+E  K  K G+PLD    +GA     Q   + +YI+ G ++GA++L GG+     
Sbjct: 312 FIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELP 371

Query: 376 -EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434
            E  GG Y++PTIF G  N MRI QEEIFGPVL+V  F T EEA+ IANDT YGL AG+W
Sbjct: 372 GELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVW 430

Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
           T D  + ++  RA++AG VWVNQY      APFGG+KQSG GR+     L  Y + K
Sbjct: 431 TRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTK 487


Lambda     K      H
   0.316    0.132    0.390 

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: 638
Number of extensions: 29
Number of successful extensions: 7
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: 497
Length of database: 501
Length adjustment: 34
Effective length of query: 463
Effective length of database: 467
Effective search space:   216221
Effective search space used:   216221
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: 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