GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Rhodanobacter denitrificans 2APBS1

Align 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized)
to candidate WP_015446956.1 R2APBS1_RS03885 aldehyde dehydrogenase

Query= SwissProt::P23105
         (486 letters)



>NCBI__GCF_000230695.2:WP_015446956.1
          Length = 527

 Score =  187 bits (474), Expect = 1e-51
 Identities = 144/429 (33%), Positives = 207/429 (48%), Gaps = 27/429 (6%)

Query: 32  IGRVHEAGRAEVDAAVRAARAALKGP-WGKMTVAERAEILHRVADGITARFGEFLEARM- 89
           +G    AG  +V AA+ AA+AA  GP W  M VAER  +LHRV + +  R  +   A + 
Sbjct: 63  LGEFGLAGDNDVQAAMCAAQAA--GPAWRAMPVAERTRLLHRVGELLEERVYDIAAAMVL 120

Query: 90  -PGHRQAEVAGQPHRHSARRANFKVFADLLKNVANEAFEMATPD----GAGALNYGVRRP 144
             G  + E  G+          F  +AD  ++ A   +    PD    G  + N  V RP
Sbjct: 121 EVGKNRMEALGEAQETVDF---FHHYADDFESHAG--YNHVLPDDPVTGFASHNASVMRP 175

Query: 145 KGVIGVISPWNLPLLLMTWKVGPALACGNCVVVKPSEETPLTATLLGEVMQAAGVPAGVY 204
            GV  VI+P+N PL L    V  AL  GN VV+K + +TP    LL + ++ AG+P GV+
Sbjct: 176 YGVWVVIAPFNFPLALAGGPVAAALVTGNTVVLKGASDTPWAGRLLADCIRDAGLPPGVF 235

Query: 205 NVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGETIMRAAAKGV--RQVSLELGGKNAGI 262
           N + G G +  G  L +HP     TFTG    G  +MR  A G   R    E+GGKN  I
Sbjct: 236 NYLSGAGRE-IGEALAQHPLTAGITFTGSVPVGRHLMRQMAGGAYPRPCIAEMGGKNPCI 294

Query: 263 VFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDAFVARLKAGAEALKIGEPND 322
           V    D+D+A  G +RSA+   GQ C    R+YV   + DA + RL A A A++IG+P  
Sbjct: 295 VTERADLDRAAAGIVRSAYGMGGQKCSALSRLYVHESVADALIGRLHAQATAIRIGDPRR 354

Query: 323 PEANFGPLISHKPREKVPSYYQQAVDDGATVVTGGGVPEMPA----HLAGGAWVQPTIWT 378
            E   GP+++    E    +     D GA V+ GG    + +     LA G +V+P +  
Sbjct: 355 HENWLGPVVNATAYENYQHHADALRDAGANVLCGGARIGLGSGGRTALARGYYVEPML-A 413

Query: 379 GLADDSAVVTEEIFGPCCHIRPFDSEEEAIELANSLPYGLASAIW--TENVRRAHRVAGQ 436
            +     +   E+F P   +  +   +EA+ LAN  P GL +  +   + V   H     
Sbjct: 414 EVPLQHPLWQHEMFLPILTVHRYGDRDEAMRLANDSPMGLTAGFYGGADEVSWFHE---H 470

Query: 437 IEAGIVWVN 445
           IEAG+ + N
Sbjct: 471 IEAGVTYAN 479


Lambda     K      H
   0.318    0.136    0.413 

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: 653
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: 527
Length adjustment: 34
Effective length of query: 452
Effective length of database: 493
Effective search space:   222836
Effective search space used:   222836
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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