GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Erythrobacter gangjinensis K7-2

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_047007132.1 AAW01_RS09770 NAD-dependent succinate-semialdehyde dehydrogenase

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



>NCBI__GCF_001010925.1:WP_047007132.1
          Length = 476

 Score =  245 bits (626), Expect = 2e-69
 Identities = 149/460 (32%), Positives = 242/460 (52%), Gaps = 15/460 (3%)

Query: 15  IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74
           I G+ V      T + INPATEE LGT+    + ++D A+ AA+      W+  +A++R 
Sbjct: 11  IAGEKVTGGGRDTEEVINPATEEVLGTLPHATSDDLDRALDAAQSGFR-EWRSTSADKRA 69

Query: 75  AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSD-----YIRTIT 129
            +L    +LI ERKE+++   + + GKP    G  +   +A    F++      Y RT+ 
Sbjct: 70  TILTNAANLIRERKEDIAGWLTREQGKPLG-DGRGEAMYSANLLEFYAQEAKRTYGRTLV 128

Query: 130 NEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMT 189
                  +V  +     PVG +    PWN P + +  K+  ALAAG +V++KP+E TP  
Sbjct: 129 RGEGSRVEVQYH-----PVGPVAGFAPWNFPAINVMRKIGGALAAGCSVIVKPSEETPAA 183

Query: 190 ATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAK 249
              L +   DAGVP G V  V G  P++    L   P +  ++FTG T  GK +   AA 
Sbjct: 184 GIALVQALLDAGVPGGAVQCVFGV-PSNVSEHLLASPIIRKLTFTGSTPVGKHLAKLAAD 242

Query: 250 TLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLE 309
            LK  + ELGG  P ++F D ++D+ ++T   + + N G+VC+   R  +E   +E F +
Sbjct: 243 DLKITTMELGGHGPVLVFDDCDVDKAVKTMAGNKYRNAGQVCVSPIRFLIEESIFEQFRD 302

Query: 310 KFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKG 369
            FV + +++ VG+  +  T +G + +    E +   I  A E G  +LTGG+      +G
Sbjct: 303 SFVERAEKVRVGNGLEDGTDMGPMANARGRENIQKLIANAKEAGANLLTGGEVIG--NQG 360

Query: 370 YFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRR 429
           +F +PT+++ +     ++  E FGPV  + P   E+ ++E+ N   YGL+A  WT+D  R
Sbjct: 361 FFHQPTVLSEVPTSADIMNNEPFGPVAILNPMSGEDAMIEEANRLPYGLAAYAWTDDAAR 420

Query: 430 AHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGG 469
             R+A ++EAG++ +N   +  +  PFGG+K SG G E G
Sbjct: 421 RRRLAAEVEAGMLAINGGSVSTVDAPFGGVKWSGYGSEDG 460


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: 592
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: 476
Length adjustment: 34
Effective length of query: 452
Effective length of database: 442
Effective search space:   199784
Effective search space used:   199784
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: 51 (24.3 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