GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Amycolatopsis halophila YIM 93223

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000504245.1:WP_034273599.1
          Length = 496

 Score =  382 bits (980), Expect = e-110
 Identities = 211/477 (44%), Positives = 291/477 (61%), Gaps = 13/477 (2%)

Query: 14  FIDGKFVPSLDGKTFDNI-NPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTAN 71
           FIDG++V +        + NPA   +L TV E    ++D AV AA++A +  PW+  TA 
Sbjct: 5   FIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATTAR 64

Query: 72  ERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNE 131
           ER  +LR++  L+   KE L+  ESLDTGK T   G +D+      F +   Y     NE
Sbjct: 65  ERGELLREIARLLQRDKEHLARTESLDTGK-TMAEGRVDVDDVTSVFRY---YANLADNE 120

Query: 132 ATQMDDVA----LNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTP 187
           A ++ D      ++  +  PVGV  LI PWN PLL M+WKLAPALAAGNTVVMKP+E+TP
Sbjct: 121 AGRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTP 180

Query: 188 MTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASA 247
           +T   L  +  +AGVP GVVNLV G G N  GA +  HPDV+ +SFTG   TGK IMA A
Sbjct: 181 LTTIELMRLVEEAGVPAGVVNLVLGGGAN-VGAPMVSHPDVDLVSFTGGLETGKKIMAMA 239

Query: 248 AKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAF 307
           A+ +KR++ ELGGKNPNV+FAD++ D  ++  + ++F + G+VC  GSR+ VE   ++ F
Sbjct: 240 AEGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEF 299

Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRP--EG 365
           + +   +   + +GD  D  T+ G L S EH ++V  +I+ A  EG  ++ GG RP    
Sbjct: 300 VAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPE 359

Query: 366 LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTN 425
           L  GYFL PT+     R+ R+V++E+FGPVVTV  FDTE+E +   NDT YGL+ +VWT+
Sbjct: 360 LADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTS 419

Query: 426 DLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482
           D  RA RVAG +  G VW+N +     +  +GG  +SGIGRE G    E Y E  +I
Sbjct: 420 DASRAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHI 476


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: 630
Number of extensions: 26
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: 496
Length adjustment: 34
Effective length of query: 452
Effective length of database: 462
Effective search space:   208824
Effective search space used:   208824
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 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