GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Rhodobacter viridis JA737

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_110805439.1 C8J30_RS08590 betaine-aldehyde dehydrogenase

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



>NCBI__GCF_003217355.1:WP_110805439.1
          Length = 483

 Score =  346 bits (888), Expect = e-100
 Identities = 192/477 (40%), Positives = 283/477 (59%), Gaps = 8/477 (1%)

Query: 19  EGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQL 78
           E   F+NG + +  +G   E + P  G  +A +     A    A+  A+A   +  W+ L
Sbjct: 6   EASHFVNGNWVEDAAGAEIEVIFPGTGEVIAILHEATPAVIEEALAGAQAAQRA--WAAL 63

Query: 79  APAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKV 138
            P +R   L R ADL+R    ELALLETLD GKPI ++S  D P  A ++ + A     +
Sbjct: 64  KPVERARILRRAADLIRARRAELALLETLDTGKPIQETSVADWPSGADSLEYFAGLAPTL 123

Query: 139 YDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198
             E  P   D      REP+GV   I  WN+P  +ACWK  PAL+TGN+++ KPSE +PL
Sbjct: 124 TGETIPLGGD-FAYTIREPLGVCVGIGAWNYPSQIACWKAAPALSTGNAMIFKPSEITPL 182

Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGE 258
            A+++A + +EAG+PAGV NV+ G G  VG  LA    V  +  TGS     ++   AG 
Sbjct: 183 GALQLAAIFVEAGMPAGVFNVVQGRG-AVGGRLATDSRVAKVSLTGSVPTGAKVYAAAG- 240

Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
           + MK + +E GGKSP IVF DA DL++A  AA     ++ G++C+ G+R+ V ++IK++F
Sbjct: 241 AGMKHVTMELGGKSPLIVFEDA-DLESAIGAAMLGNFYSSGQICSNGTRVFVHKAIKERF 299

Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEET 378
           L  + E     K G+PLD  T  G LV   Q   VL YI     +GA+L+ GG    E  
Sbjct: 300 LTRLAERTAAIKAGDPLDETTQFGPLVSAAQHAKVLGYIATAKSEGARLVCGGAAGAE-- 357

Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438
           G  +V+PT+F  VT++M IA+EE+FGPV++V+ F+T +E +A AN T +GLAAG++T+D+
Sbjct: 358 GALFVQPTVFADVTDSMTIAREEVFGPVMAVLDFETEDEVIARANGTDFGLAAGVFTADL 417

Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWI 495
           ++ H+    ++AG+ W+N Y+   +  PFG  K SG GR+ S  A+E YT++KA ++
Sbjct: 418 ARGHRVIAQLQAGTTWINAYNLTPVEMPFGAVKSSGVGRENSKAAIEHYTQVKAVYV 474


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: 627
Number of extensions: 30
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: 497
Length of database: 483
Length adjustment: 34
Effective length of query: 463
Effective length of database: 449
Effective search space:   207887
Effective search space used:   207887
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 24 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