GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Trichormus variabilis ATCC 29413

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  315 bits (808), Expect = 2e-90
 Identities = 181/483 (37%), Positives = 282/483 (58%), Gaps = 9/483 (1%)

Query: 8   PIDCLHFIDGKFVPSLDGKTFDNINPATEEKL-GTVAEGGAAEIDLAVQAAKKALNGPWK 66
           P++C ++I+G+++ +    T ++ NPA + ++  T     A + D AV AA++A  G W+
Sbjct: 4   PLNCQNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAY-GSWR 62

Query: 67  KMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIR 126
           K+ A  R   + +VG+L+L+ KEEL+ L S + GKP   +   D+        + +   R
Sbjct: 63  KVPAPARAEYIFRVGELLLQHKEELAQLISREMGKPITEARG-DVQEGVDCAFYSAGEGR 121

Query: 127 TITNEATQMD-DVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAEL 185
            +  + T  +        +R P+GV  LI PWN P+ +  WK  PAL  GNTV++KPAE 
Sbjct: 122 RLFGQTTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAED 181

Query: 186 TPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA 245
           TP  AT L EI   AG+P GV+NLVHG G   AG AL EHP+++ +SFTG + TG  +  
Sbjct: 182 TPACATKLIEIFAAAGLPPGVINLVHGVG-EEAGKALVEHPNIDLVSFTGSSATGAYVGE 240

Query: 246 SAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYE 305
           +  +T KR+  E+GGKN  V+  D++L+  ++  +  +F   G+ C   SR+ + R   E
Sbjct: 241 TCGRTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKE 300

Query: 306 AFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK-RPE 364
            F      +T +L +G   + +T +G +I++   +RV  Y+ +A EEG  IL GG+   E
Sbjct: 301 KFTTMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTE 360

Query: 365 G-LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423
           G L++GYF +PTI+  +T   RV +EEIFGPVV +I   T EE +  +NDT YGLS+SV+
Sbjct: 361 GQLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVY 420

Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFL-RDLRTPFGGMKQSGIG-REGGLHSFEFYSELTN 481
           T D+ RA      IE GI ++N   +  ++  PFGG+KQ+G G RE G  + + ++E  +
Sbjct: 421 TRDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKS 480

Query: 482 ICI 484
           + +
Sbjct: 481 VYV 483


Lambda     K      H
   0.318    0.136    0.404 

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: 585
Number of extensions: 27
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: 486
Length of database: 498
Length adjustment: 34
Effective length of query: 452
Effective length of database: 464
Effective search space:   209728
Effective search space used:   209728
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 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