GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase

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



>NCBI__GCF_001592305.1:WP_068168204.1
          Length = 485

 Score =  363 bits (933), Expect = e-105
 Identities = 198/483 (40%), Positives = 289/483 (59%), Gaps = 8/483 (1%)

Query: 6   VKPIDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPW 65
           + P     FI+G+ V    G+ F+++NPAT      V E    +++ AV+AA       W
Sbjct: 1   MNPTTLFSFINGQTVNG-GGQVFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGF-ALW 58

Query: 66  KKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYI 125
             M+A ER  +LR+  D++ ER  EL+ LE  D GKP   +  +D+   A    +F+   
Sbjct: 59  SAMSATERGRILRRAADILRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAA 118

Query: 126 RTITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAEL 185
            T+T +   + + A  Y  + P+GV   I  WN P+ +  WK APALAAGN ++ KP+EL
Sbjct: 119 ATLTGQQYPLKN-AFAYTRKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEL 177

Query: 186 TPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA 245
           TP TA  LAE+  +AGVP GV N+V G G  + GA L  HPDV  +S TG   TGK +M 
Sbjct: 178 TPATAVKLAEVYLEAGVPPGVFNVVQGRG--AVGAMLAAHPDVAKVSVTGSVPTGKRVME 235

Query: 246 SAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYE 305
           +AA TLKR++ ELGGK+P ++F D++L++ +   M  +F  QGEVC   +R++V+R    
Sbjct: 236 TAAGTLKRVTMELGGKSPLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRGIAP 295

Query: 306 AFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKR--P 363
            FL +   +T  L VGDP D  T++GALIS+ H  RV  YI     EG T++ GG+R   
Sbjct: 296 RFLARLKERTLLLRVGDPTDPDTEIGALISEAHTARVMDYIASGQAEGATLVCGGERVAV 355

Query: 364 EGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423
           EGL    F+ PTI      D R+V+EEIFGPV++++ FDTE E + + N + + L+A V+
Sbjct: 356 EGL-GDQFVAPTIFADCRDDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVF 414

Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483
           T DL+R HRVA QI AGI W+N + +  +  PFGG+ +SGIG E  + + + Y++L  + 
Sbjct: 415 TTDLQRGHRVAAQIRAGICWINNYNITPIEMPFGGVGESGIGSENSMAALDHYTQLKTVY 474

Query: 484 IKL 486
           ++L
Sbjct: 475 VEL 477


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: 555
Number of extensions: 22
Number of successful extensions: 4
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: 485
Length adjustment: 34
Effective length of query: 452
Effective length of database: 451
Effective search space:   203852
Effective search space used:   203852
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