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_012592831.1 MSIL_RS19705 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000021745.1:WP_012592831.1
          Length = 507

 Score =  437 bits (1125), Expect = e-127
 Identities = 234/484 (48%), Positives = 311/484 (64%), Gaps = 12/484 (2%)

Query: 20  PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTS 78
           P  + I+ ++V+S S KTF    P+T E+I  V E  + D+D AV AA  AF S  WS  
Sbjct: 25  PRPMLIDGKWVKSVSGKTFDVFDPATGEKIASVAEGDAADVDLAVAAARRAFESGPWSRM 84

Query: 79  DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKI 137
            P  R ++++++ DLI +HAD LA IE+LDNGK    +K  DV L+A  F   +GW  K+
Sbjct: 85  TPSERGRIIHRIGDLILDHADELAAIESLDNGKPKAVAKAADVTLSADMFHYMSGWATKL 144

Query: 138 KGSVIET------GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKT 191
           +G  I        G    + TR EPIGV GQIIPWNFPLLMA+WKL P L TGC  VLK 
Sbjct: 145 EGKHIPISALTAPGMEFVSMTRLEPIGVVGQIIPWNFPLLMAAWKLAPALTTGCAVVLKI 204

Query: 192 AESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHI 251
           AE TPLSAL L  L+ EAG P GVVN+V GFG TAGA ++ HP + KVAFTGST  GR I
Sbjct: 205 AEETPLSALRLGELLIEAGVPDGVVNIVPGFGETAGAALAGHPGVDKVAFTGSTEVGRLI 264

Query: 252 MKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEG 311
           ++AA+  +LKKV+LELGGKSPNIV  DAD +  I      IF+N G+ C AGSR++VQ  
Sbjct: 265 VQAASR-DLKKVSLELGGKSPNIVLGDADPEMAIAGATAAIFFNHGQCCNAGSRLFVQRN 323

Query: 312 IYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGER 371
           ++DK+V      AE +K+G     +T MG   S++Q D++   +  G++EGA  + GGE 
Sbjct: 324 LFDKVVEGIAAQAEKIKLGHGLNAETEMGPLVSRVQYDRVTGLLASGRQEGARAVCGGEG 383

Query: 372 FGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEE-VIALANDSEYGLAAGVH 430
            G  GYF+ PT+  D     ++VR+EIFGPV+  T F   ++ +IA AN++ YGLAAGV 
Sbjct: 384 LGGAGYFVPPTVLVDTNPGMRVVREEIFGPVLVATPFDEPDDALIAEANNTIYGLAAGVW 443

Query: 431 TTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV- 489
           + N   A  ++N++ +GT+W+N Y+ F   +PFGGY QSG GREMG+  L NY + KA+ 
Sbjct: 444 SGNTGRAHQIANRLRAGTVWINCYHVFDAALPFGGYKQSGWGREMGQAVLSNYLEAKAIT 503

Query: 490 -RIG 492
            RIG
Sbjct: 504 TRIG 507


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: 647
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: 495
Length of database: 507
Length adjustment: 34
Effective length of query: 461
Effective length of database: 473
Effective search space:   218053
Effective search space used:   218053
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.

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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