GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Magnetospirillum magneticum AMB-1

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein

Query= reanno::acidovorax_3H11:Ac3H11_612
         (483 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385953.1 AMB_RS18195 DUF1487
           domain-containing protein
          Length = 496

 Score =  275 bits (702), Expect = 3e-78
 Identities = 181/478 (37%), Positives = 259/478 (54%), Gaps = 10/478 (2%)

Query: 8   LSPRHLINGRW-EIGTTTGISTNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQST 66
           LS +HLI G+    G       +   T E++   A   +   ++AV +A  A   W++ +
Sbjct: 16  LSGKHLIGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKDWAKQS 75

Query: 67  PQRRADVLDMIGSELLARKDELGALLAREEGKTL-PEGVAEVARSGQIFKFFAGEALRIQ 125
            + R  ++   G  L A  +ELG L+A E GK L  E   E      +F FF G    ++
Sbjct: 76  ARARGKLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELK 135

Query: 126 GELLASVRQGVQVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPA 185
           GE +      + V V REPVGVVG I PWN P  + A K A AL  GN+VV K AE  P 
Sbjct: 136 GETIPFNPDMLTVTV-REPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPL 194

Query: 186 CGWALAEIISRSGLPAGAFNLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAASQ 245
               +AEI++ + LP G FN++ G G E G  LV+HP V  ++FTGSV TG  + +AA++
Sbjct: 195 TVLRVAEIMN-TVLPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAE 253

Query: 246 RRAKVQLEMGGKNPLIVLADADLDQAVDCALQGSYFS-TGQRCTASSRLIVEAEVHDAFV 304
           +   V LE+GGK+P+IV ADAD+DQAV  AL G  F+  GQ CTASSRL V   +HD FV
Sbjct: 254 KLIPVTLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFV 313

Query: 305 ARLRNRLASLKVGHALERGTEMGPVVDDNQLAQNLGYIDIA-KSEGA-EHVWGGERLE-R 361
           A+++ ++ ++ +G  L+  T++G +V D QL +   YI I  +++GA +HV      + +
Sbjct: 314 AKVKAKVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTDPK 373

Query: 362 PTPGHYMSPALFLA-RPEHRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTT 420
              G ++ P +F   +   R+ +EEIFGPV  V++  DY+  LA AND+ +GL A I T 
Sbjct: 374 LAKGRFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTR 433

Query: 421 SLKRAMHFKRHAAVGMTMVNLPTAGVDFHVPFGGRKESSYGAREQGRYAAEFYTTVKT 478
             K AM   +    G   VN     V   + +GG K S  G         E +T  KT
Sbjct: 434 DFKLAMDATKRLEAGFVQVN-QNLVVQPGLSYGGVKTSGIGKEASLESMLEHFTHKKT 490


Lambda     K      H
   0.320    0.135    0.400 

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: 517
Number of extensions: 29
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: 483
Length of database: 496
Length adjustment: 34
Effective length of query: 449
Effective length of database: 462
Effective search space:   207438
Effective search space used:   207438
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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