GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF 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)



>NCBI__GCF_000009985.1:WP_011385953.1
          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.

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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