GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Trichormus variabilis ATCC 29413

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  302 bits (774), Expect = 2e-86
 Identities = 173/482 (35%), Positives = 274/482 (56%), Gaps = 17/482 (3%)

Query: 23  FINGEYTDAVSGETFECLSPVD-GRFLAKVASCDLADANRAVENARATFNSGVWSQLAPA 81
           +ING++ +A +  T    +P +    +A        D +RAV  AR  + S  W ++   
Sbjct: 10  YINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGS--WRKVPAP 67

Query: 82  KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141
            R   + R  +LL ++ EELA L + +MGKPI ++   D+        ++A    +++ +
Sbjct: 68  ARAEYIFRVGELLLQHKEELAQLISREMGKPITEARG-DVQEGVDCAFYSAGEGRRLFGQ 126

Query: 142 VAPTPH-DQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200
             P+   ++  +  R P+GV   I PWNFP+ + CWK  PAL  GN+V+LKP+E +P  A
Sbjct: 127 TTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACA 186

Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGES- 259
            ++ ++   AG+P GV+N++ G G   GKAL  H ++D + FTGS+        Y GE+ 
Sbjct: 187 TKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATG----AYVGETC 242

Query: 260 --NMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317
               KR+ LE GGK+  +V  DA DL+ A + A        G+ CTA SRL++ R IK+K
Sbjct: 243 GRTHKRVCLEMGGKNAQVVMEDA-DLELALDGALWGAFGTTGQRCTATSRLILHRDIKEK 301

Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377
           F  M+ E     + G   +P+T +G +++ +Q+  V  Y+    ++GAK+L GG+   E 
Sbjct: 302 FTTMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEG 361

Query: 378 --TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435
               G + +PTI D VT  MR+A+EEIFGPV+++I   T EEA+AI NDT YGL++ ++T
Sbjct: 362 QLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYT 421

Query: 436 SDISKAHKTARAVRAGSVWVN-QYDGGDMTAPFGGFKQSGNG-RDKSLHALEKYTELKAT 493
            DI++A    R +  G  ++N    G ++  PFGG KQ+GNG R+    AL+ +TE K+ 
Sbjct: 422 RDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKSV 481

Query: 494 WI 495
           ++
Sbjct: 482 YV 483


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: 595
Number of extensions: 24
Number of successful extensions: 6
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: 498
Length adjustment: 34
Effective length of query: 463
Effective length of database: 464
Effective search space:   214832
Effective search space used:   214832
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 Apr 09 2024. 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