GapMind for catabolism of small carbon sources

 

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

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_011384937.1 AMB_RS12865 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase

Query= curated2:Q9X448
         (316 letters)



>NCBI__GCF_000009985.1:WP_011384937.1
          Length = 469

 Score =  385 bits (989), Expect = e-111
 Identities = 204/304 (67%), Positives = 235/304 (77%)

Query: 12  YDRLIAAARAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVAAEHRLD 71
           ++ +IA     AP    V HPCD+ SL G +EAA++GLI PIL+ PEAKIR+VA E  LD
Sbjct: 164 FEDIIARCHTLAPISVAVCHPCDQVSLEGPVEAAKLGLIDPILIGPEAKIRSVAKEFNLD 223

Query: 72  LGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRTQRRISH 131
           +    IVD  HSH +A KAVA+ R G  E LMKGSLHTDE+MHEVA+   GLRT RRISH
Sbjct: 224 IEGLRIVDTQHSHESAEKAVAMCRSGEAEALMKGSLHTDEMMHEVASRDKGLRTARRISH 283

Query: 132 VFVMDVPGHTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLGEPRVAILSAVETVT 191
           VFVMDVP +  TL ITDAAINI+P LE K DI+QNAI+L   +G+  P+VAILSAVETV 
Sbjct: 284 VFVMDVPTYPRTLLITDAAINIYPTLEDKADILQNAIELAHVLGVELPKVAILSAVETVY 343

Query: 192 AKIPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKGINSPVAGHAQILVVP 251
            KI STIEAAALCKMA+RGQITG  L+GPLAFDNAI +EAA+IK INSPVAG A IL+VP
Sbjct: 344 PKINSTIEAAALCKMADRGQITGAQLDGPLAFDNAISEEAAKIKKINSPVAGRADILLVP 403

Query: 252 DLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLASCAVAALYAARRRAA 311
           DLEAGNMLAK L++L  ADAAG+VLGARVPIVLTSRADS + RLASCAVA L+A  RRA 
Sbjct: 404 DLEAGNMLAKQLSYLADADAAGIVLGARVPIVLTSRADSAKARLASCAVAVLFAHARRAK 463

Query: 312 QVAA 315
              A
Sbjct: 464 SAVA 467


Lambda     K      H
   0.320    0.133    0.376 

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: 337
Number of extensions: 8
Number of successful extensions: 1
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: 316
Length of database: 469
Length adjustment: 30
Effective length of query: 286
Effective length of database: 439
Effective search space:   125554
Effective search space used:   125554
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 (21.9 bits)
S2: 50 (23.9 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