GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Pseudarthrobacter sulfonivorans Ar51

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase

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



>NCBI__GCF_001484605.1:WP_058929223.1
          Length = 508

 Score =  391 bits (1004), Expect = e-113
 Identities = 210/478 (43%), Positives = 293/478 (61%), Gaps = 7/478 (1%)

Query: 24  INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83
           I+G +  + SGETF C+ P D     +V +  + D +RAV  AR  F+ G W Q  P++R
Sbjct: 25  IDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWPQTLPSQR 84

Query: 84  KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143
            A L RFADLL +N +ELA  +  + GK IG+ +   +    Q  H+ A   + +     
Sbjct: 85  AALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQ-MGQHAHYVAGLAETIQGRTI 143

Query: 144 PTPHDQLGLVT-REPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
            +        T REP+GVV  I PWN PL++  WKL  ALA GN+VV+KPSE +P + +R
Sbjct: 144 ESNWPNTAAFTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEATPTSTLR 203

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           +A+LA+EAG P GV+NV+ G+G   G AL  H  VD + FTGST   + +   A E    
Sbjct: 204 MAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGRAINKQAAE-RFA 262

Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322
           R+ LE GGKSPNI+F+DA D+  A   A + I    G+ C  GSR+LV+ SI D F+  +
Sbjct: 263 RVTLELGGKSPNIIFSDA-DIDNAVHGAMAGIFGATGQTCMGGSRVLVQDSIYDDFVDRM 321

Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKR---TLEETG 379
             A +    G+PLDP   +G + +  Q   V+ Y++ G  +GA+++AGG R   T E + 
Sbjct: 322 ARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGARCMTTSELSK 381

Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439
           G + EPT+F  V+N  R+AQEEIFGPV S+I F   +EAV IAN + +GLAAG+WT+D+S
Sbjct: 382 GLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFGLAAGVWTNDVS 441

Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
           +AH+  R VR+G+VWVN Y   + + PFGGFKQSG GR+    AL+ YTE+K+ WI L
Sbjct: 442 RAHRMIRRVRSGTVWVNTYRLTNYSVPFGGFKQSGIGRELGPDALDAYTEVKSAWIDL 499


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: 609
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: 497
Length of database: 508
Length adjustment: 34
Effective length of query: 463
Effective length of database: 474
Effective search space:   219462
Effective search space used:   219462
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