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_012757049.1 RLEG_RS07320 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000023185.1:WP_012757049.1
          Length = 506

 Score =  350 bits (898), Expect = e-101
 Identities = 191/479 (39%), Positives = 283/479 (59%), Gaps = 16/479 (3%)

Query: 7   KPIDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPW 65
           K  D    IDG++         + + P+    +     G   + + A+ AA+KA + GPW
Sbjct: 14  KARDFKMLIDGRWEAGASDP-IERVAPSHGVVVSRFPTGSRKDAERAISAARKAFDLGPW 72

Query: 66  KKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTW-----LSGSIDIPRAAYNFHF 120
            +MTA+ER A+L K  DLI  R EEL+ L++++ GKP       ++GS+DI R A     
Sbjct: 73  PRMTASERSAILLKAADLIAARAEELAFLDAIEAGKPITQVRGEIAGSVDIWRYA----- 127

Query: 121 FSDYIRTITNEA-TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVV 179
            +   R +  E+   + D  L   +R  +GV+ +I PWN P L++  KL  ALAAG T V
Sbjct: 128 -AALARDLHGESYNTLGDGTLGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTV 186

Query: 180 MKPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTT 239
           +KP+ELT  +  VL EI + AG+PDGVVN+V G GP   GA +T HPDV+ +SFTG T  
Sbjct: 187 VKPSELTSGSTLVLGEILQQAGIPDGVVNIVTGTGPE-VGAIMTSHPDVDMVSFTGSTGV 245

Query: 240 GKIIMASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYV 299
           GK+ M++AA+TLK++S ELGGKNP ++F D++L   I+  +  ++ N GE C  GSR+ +
Sbjct: 246 GKLTMSNAAQTLKKVSLELGGKNPQIVFPDADLGAFIDAAVFGAYFNAGECCNAGSRLIL 305

Query: 300 ERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTG 359
            +      +++    +K + VGDP D  T+VGA+I+ +H E+++GY+  A   G  +  G
Sbjct: 306 HKSIASDVVKRIAELSKAVKVGDPLDPSTQVGAIITPQHLEKISGYVAGARSSGARVAHG 365

Query: 360 GKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLS 419
           G+  + L  G F+ PTI+  +T D  V +EE+FGPV++V+ F+T  E +   N   YGLS
Sbjct: 366 GETLD-LGMGQFMSPTILEEVTPDMAVAREEVFGPVLSVLTFETSAEAIRIANSIDYGLS 424

Query: 420 ASVWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478
           A VW+ D      +   + AG VW+NT+       PFGG KQSG+GRE G H+ E Y+E
Sbjct: 425 AGVWSRDFDTCLTIGRSVRAGTVWMNTFMDGASELPFGGYKQSGLGRELGRHAVEDYTE 483


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: 681
Number of extensions: 33
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: 506
Length adjustment: 34
Effective length of query: 452
Effective length of database: 472
Effective search space:   213344
Effective search space used:   213344
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