GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Halomonas xinjiangensis TRM 0175

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_043532311.1 JH15_RS16505 NAD-dependent succinate-semialdehyde dehydrogenase

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



>NCBI__GCF_000759345.1:WP_043532311.1
          Length = 487

 Score =  298 bits (764), Expect = 2e-85
 Identities = 175/478 (36%), Positives = 271/478 (56%), Gaps = 9/478 (1%)

Query: 22  AFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPA 81
           A+I+G +  A SGE  +  +P +G  + +V     A+  RA+  A A F +  W      
Sbjct: 14  AYIDGSWVAADSGEQIDVFNPANGEVIGRVPRLGRAETERAITAADAAFPA--WRAHTAQ 71

Query: 82  KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141
           +R   L+++ DL+ ++ EELA + TL+ GKP+ +++  +I  AA  + W AE   ++Y E
Sbjct: 72  ERADILMKWHDLMHEHQEELATIMTLEQGKPLKEAAG-EIAYAASFLRWFAEEARRMYGE 130

Query: 142 VAPTPH-DQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200
             P    +Q  ++T++PVGVVGAI PWNFP  M   K+G ALA G  +V+KP+ ++P +A
Sbjct: 131 TIPAAKPNQRIVITKQPVGVVGAITPWNFPAAMITRKVGAALAAGCPIVVKPASQTPFSA 190

Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESN 260
             +A LA  AG+P GV NV+ G    +  AL    +V  + FTGST++ +QLM  A + +
Sbjct: 191 TALALLAERAGVPRGVFNVVTGSAREIAAALTESPEVRKITFTGSTEVGRQLMSQASQ-H 249

Query: 261 MKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLP 320
           +++I LE GG +P IVF DA DL AA + A +A   N G+ C   +R LV+ S+ + F  
Sbjct: 250 IQKISLELGGNAPFIVFEDA-DLDAAVDGAMAAKFRNGGQTCVCTNRFLVQSSVVNAFCE 308

Query: 321 MVVEALKG-WKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETG 379
            +  A+    + G+ L     +G L+D   +  V +++      GA+LL GG       G
Sbjct: 309 KLAVAMNSELRVGDGLKDDVNIGPLIDADGVEKVSAHVHDAVDKGAELLLGGNP--HPLG 366

Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439
           G +  PT+ +G    M +AQEE FGP+ +V  FD  E+AVA+ANDT +GLA+  ++ D++
Sbjct: 367 GNFFTPTLVNGANADMLVAQEETFGPLAAVFPFDDEEDAVAMANDTQFGLASYFYSRDLA 426

Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
           +  + A ++  G V +N     +  APFGG K SG GR+     LE++ E K   I L
Sbjct: 427 RVWRVAESLEYGMVGINTGLISNAAAPFGGVKASGLGREGGRQGLEEFVETKYLCIDL 484


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: 554
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: 487
Length adjustment: 34
Effective length of query: 463
Effective length of database: 453
Effective search space:   209739
Effective search space used:   209739
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