GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Magnetospirillum magneticum AMB-1

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein

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



>NCBI__GCF_000009985.1:WP_011385953.1
          Length = 496

 Score =  328 bits (840), Expect = 3e-94
 Identities = 186/470 (39%), Positives = 266/470 (56%), Gaps = 7/470 (1%)

Query: 7   KPIDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWK 66
           K +   H I GK VP+  G+ F+  NPAT E +GT A G   ++D+AV +AK A    W 
Sbjct: 14  KALSGKHLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKD-WA 72

Query: 67  KMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIR 126
           K +A  R  ++ + G ++    EEL  L +L+TGK       ++    A  F FF     
Sbjct: 73  KQSARARGKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGS 132

Query: 127 TITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELT 186
            +  E    +   L   +R PVGV+G I PWN+PLLLM  K A AL AGN+VV+K AE  
Sbjct: 133 ELKGETIPFNPDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEA 192

Query: 187 PMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMAS 246
           P+T   +AEI     +P G+ N++ GFGP   GA L EHPDV  ++FTG   TG+I+  +
Sbjct: 193 PLTVLRVAEIMNTV-LPPGLFNMLSGFGPE-CGAPLVEHPDVKKVTFTGSVETGRIVYKA 250

Query: 247 AAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSS-FINQGEVCLCGSRIYVERPAYE 305
           AA+ L  ++ ELGGK+P ++ AD+++D+ +   +    F  QG+ C   SR++V    ++
Sbjct: 251 AAEKLIPVTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHD 310

Query: 306 AFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGT---ILTGGKR 362
            F+ K  AK   +V+GDP D KT +G ++SD   ERV  YIK+  E  G    + +    
Sbjct: 311 EFVAKVKAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPT 370

Query: 363 PEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASV 422
              L KG F++P I TG+    R+ +EEIFGPV  VI +   E+VL Q ND+ YGL+AS+
Sbjct: 371 DPKLAKGRFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASI 430

Query: 423 WTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHS 472
           WT D + A     ++EAG V VN   +      +GG+K SGIG+E  L S
Sbjct: 431 WTRDFKLAMDATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLES 480


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: 551
Number of extensions: 23
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: 486
Length of database: 496
Length adjustment: 34
Effective length of query: 452
Effective length of database: 462
Effective search space:   208824
Effective search space used:   208824
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 Sep 17 2021. 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