GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Rhizobium leguminosarum bv. trifolii WSM1325

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_012759625.1 RLEG_RS21595 NAD-dependent succinate-semialdehyde dehydrogenase

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



>NCBI__GCF_000023185.1:WP_012759625.1
          Length = 493

 Score =  350 bits (897), Expect = e-101
 Identities = 191/480 (39%), Positives = 277/480 (57%), Gaps = 21/480 (4%)

Query: 14  FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73
           +IDG +      +TFD +NPAT E L ++ + GAAE   A+ AA  A  G W    A ER
Sbjct: 23  YIDGVWTSGDATRTFDVLNPATGELLASLPDMGAAETRTAIDAAHAAQPG-WAARPAKER 81

Query: 74  IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133
             +LRK  DL++   +EL+ + + + GKP         P A     + + YI     EA 
Sbjct: 82  STILRKWFDLMVANADELAAILTAEMGKP--------FPEARGEILYAAAYIEWYAEEAK 133

Query: 134 QM---------DDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAE 184
           ++         DD  +   IR+PVGV+G I PWN P  ++T K+APALA G TVV KPAE
Sbjct: 134 RIYGETIPAPSDDKRM-IVIRQPVGVVGTITPWNFPAAMITRKIAPALAVGCTVVSKPAE 192

Query: 185 LTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIM 244
            TP+TA  LA +   AG+P GV N++ G    + G  L  +  V  ISFTG T  G+I+M
Sbjct: 193 QTPLTAIALAVLAEQAGIPAGVFNVIVGVDGPAIGRELCGNEKVRKISFTGSTEVGRILM 252

Query: 245 ASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAY 304
              A  +K++S ELGG  P ++F D++LD  +E  + S + N G+ C+C +R+YV+   Y
Sbjct: 253 RQCADQIKKVSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRLYVQSNVY 312

Query: 305 EAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE 364
           +AF  K  AK  E+ VGD F     +G LI ++   +V  ++  A+ +G  +LTGGKR +
Sbjct: 313 DAFAAKLAAKVAEMSVGDGFKPGVVIGPLIDEQGLAKVEDHVSDALAKGAKVLTGGKRID 372

Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424
           G   G F  PT++TG+ R  +V +EE FGPV  +  F+T E+V+ Q NDT +GL+A  + 
Sbjct: 373 G--AGTFFTPTVLTGVARGMKVAREETFGPVAPLFRFETVEDVIAQANDTEFGLAAYFYA 430

Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
            DL++  RVA  +E G++ +NT  +     PFGG+KQSG+GREG  H  + Y E+  +CI
Sbjct: 431 GDLKKVWRVAEALEYGMIGINTGLMSSETAPFGGIKQSGLGREGSRHGADDYLEMKYLCI 490


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: 601
Number of extensions: 29
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: 493
Length adjustment: 34
Effective length of query: 452
Effective length of database: 459
Effective search space:   207468
Effective search space used:   207468
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.

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