GapMind for catabolism of small carbon sources

 

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

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>NCBI__GCF_001592305.1:WP_068168204.1
          Length = 485

 Score =  347 bits (890), Expect = e-100
 Identities = 201/482 (41%), Positives = 282/482 (58%), Gaps = 11/482 (2%)

Query: 20  PTGLF--INNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWST 77
           PT LF  IN + V    +  F +V+P+T      V+EA  +D++ AVEAA A F + WS 
Sbjct: 3   PTTLFSFINGQTVNGGGQ-VFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGF-ALWSA 60

Query: 78  SDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTDK 136
                R ++L + AD++ E    LA +E  D GK +      DV   A      AG    
Sbjct: 61  MSATERGRILRRAADILRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAAAT 120

Query: 137 IKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTP 196
           + G      +  F YTR+EP+GVC  I  WN+P+ +A WK  P L  G   + K +E TP
Sbjct: 121 LTGQQYPLKNA-FAYTRKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSELTP 179

Query: 197 LSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAA 256
            +A+ LA +  EAG PPGV NVV G G   GA +++HP + KV+ TGS  TG+ +M+ AA
Sbjct: 180 ATAVKLAEVYLEAGVPPGVFNVVQGRG-AVGAMLAAHPDVAKVSVTGSVPTGKRVMETAA 238

Query: 257 ESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
              LK+VT+ELGGKSP +VFDDAD++  +   + G FY  GEVC   +R++VQ GI  + 
Sbjct: 239 -GTLKRVTMELGGKSPLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRGIAPRF 297

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKG 376
           ++  K     L++GDP   DT +GA  S+    +++ YI  G+ EGAT++ GGER   +G
Sbjct: 298 LARLKERTLLLRVGDPTDPDTEIGALISEAHTARVMDYIASGQAEGATLVCGGERVAVEG 357

Query: 377 Y---FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTN 433
               F+ PTIF D ++D +IVR+EIFGPV+++  F T  E IA AN S + LAAGV TT+
Sbjct: 358 LGDQFVAPTIFADCRDDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVFTTD 417

Query: 434 LSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493
           L     V+ +I +G  W+N YN     +PFGG  +SGIG E    ALD+YTQ+K V + L
Sbjct: 418 LQRGHRVAAQIRAGICWINNYNITPIEMPFGGVGESGIGSENSMAALDHYTQLKTVYVEL 477

Query: 494 SQ 495
            +
Sbjct: 478 GE 479


Lambda     K      H
   0.316    0.133    0.389 

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: 567
Number of extensions: 32
Number of successful extensions: 6
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: 495
Length of database: 485
Length adjustment: 34
Effective length of query: 461
Effective length of database: 451
Effective search space:   207911
Effective search space used:   207911
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.

Links

Downloads

Related tools

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