GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Methylocella silvestris BL2

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012590504.1 MSIL_RS07550 2-hydroxymuconic semialdehyde dehydrogenase

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



>NCBI__GCF_000021745.1:WP_012590504.1
          Length = 504

 Score =  308 bits (789), Expect = 3e-88
 Identities = 192/485 (39%), Positives = 265/485 (54%), Gaps = 19/485 (3%)

Query: 24  FINNEFVQS-KSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQV 82
           FIN EF Q   SK  +   SP     I +V E    ++D AV AA AA   +W       
Sbjct: 24  FINGEFTQGLTSKGWWENRSPLDNSVIGRVPEGGQAEVDAAVHAARAALDGTWGKMTVAQ 83

Query: 83  RMKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKIKGSV 141
           R  +L  +A+ ID   D     E LD GK   + S  D+   AA F+  A   D +K   
Sbjct: 84  RTDLLAAVANEIDARFDEFLAAECLDTGKPYSLASHIDIPRGAANFKMFA---DTVKNVS 140

Query: 142 IET-------GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194
            ET       G +  NY  R P G+   I PWN PLL+ +WK+GP L  G T V+K +E 
Sbjct: 141 TETFILDTPDGKSAVNYGLRRPKGLIAVISPWNLPLLLMTWKVGPALACGNTVVVKPSEE 200

Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGP-TAGAPISSHPKIKKVAFTGSTATGRHIMK 253
           TPL+A  L  ++ + G P GV NVV G GP +AG  ++ HP +  + FTG T TG  IM+
Sbjct: 201 TPLTATLLGEVMNKVGVPKGVYNVVHGLGPNSAGEFLTQHPLVNGITFTGETRTGEAIMR 260

Query: 254 AAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIY 313
            AA   +++V+ ELGGK+P IVF D D+   I+  +   F N G+VC    R+YV+  I+
Sbjct: 261 QAA-LGVRQVSFELGGKNPAIVFADCDLDKAIEGTMRSAFANCGQVCLGTERVYVERPIF 319

Query: 314 DKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG---E 370
           D  V+  K  AE+L++G P    T +G   SQ    K+L Y  +  +EGAT++TGG   +
Sbjct: 320 DSFVARMKGDAEALRLGRPEDGATNLGPLISQEHRSKVLSYYKLALEEGATLVTGGGVPD 379

Query: 371 RFGN--KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAG 428
             G    G +++PTI+  +K+D + V +EIFGP   I  F T EE + LAN + YGLAA 
Sbjct: 380 MPGELALGAWVQPTIWTGLKDDARAVNEEIFGPCCHIRPFDTEEEAVRLANSTPYGLAAA 439

Query: 429 VHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKA 488
           V T N+S A  V++K++ G  WVN++        FGG  QSGIGRE G  +L+ YT++  
Sbjct: 440 VWTENVSRAHRVASKMDVGICWVNSWFLRDLRTAFGGAKQSGIGREGGLHSLEFYTELSN 499

Query: 489 VRIGL 493
           V I L
Sbjct: 500 VCIKL 504


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: 579
Number of extensions: 31
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: 504
Length adjustment: 34
Effective length of query: 461
Effective length of database: 470
Effective search space:   216670
Effective search space used:   216670
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