GapMind for catabolism of small carbon sources

 

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

Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thiolase

Query= reanno::pseudo5_N2C3_1:AO356_21640
         (393 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385133.1 AMB_RS13850
           3-oxoadipyl-CoA thiolase
          Length = 400

 Score =  338 bits (866), Expect = 2e-97
 Identities = 192/401 (47%), Positives = 268/401 (66%), Gaps = 11/401 (2%)

Query: 1   MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQ-TGLSGEQVDEVILGQVLTA 59
           M E +I   TRT IG + GSLA +   +L A  I+ L+ +  GL   +VDEV  G    A
Sbjct: 1   MTEALICDYTRTPIGRYAGSLAGVRTDDLAAHPIKALMARHAGLDWSRVDEVAYGCANQA 60

Query: 60  GS-GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118
           G   +N AR A +LAGLPH++   TLN++CGSG+ A+   A+A+  G+AE++IAGG+E+M
Sbjct: 61  GEDNRNVARMALLLAGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVESM 120

Query: 119 SLAPYVLPAARTGLRMGHAKMIDSMI----TDGLWD-AFNDYHMGITAENLVDKYGISRE 173
           S AP+V+  A +      A++ D+ I     + L + A+    M  TAEN+ +++ ISRE
Sbjct: 121 SRAPFVMNKADSAFSRD-ARLYDTTIGWRFVNALMEKAYGTDSMPETAENVAEQFNISRE 179

Query: 174 EQDAFAAASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLK 233
           +QDAFAA SQ KA AA + GRFA EI+P+ +P RKGDPV  + DE PR  TT E+L KLK
Sbjct: 180 DQDAFAARSQAKASAAQKNGRFAQEISPVTLPARKGDPVVVSHDEHPRE-TTVEALAKLK 238

Query: 234 PAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGP 293
             F+  GS+TAGNAS +NDGAAA+++ S   AKA GL  +A+I   A AGV+P IMGIGP
Sbjct: 239 APFRAGGSITAGNASGVNDGAAALLIASPAAAKAHGLTPIARILGMATAGVEPRIMGIGP 298

Query: 294 VSATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKW--DMDKVNVNGGAIALGHPI 351
           V AT++ L + G ++  LD++E NEAFAAQ+LA  R+L    D  +VN NGGAIALGHP+
Sbjct: 299 VPATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADDDQRVNPNGGAIALGHPL 358

Query: 352 GASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           G SG R++ +   ++ +   ++ L+T+CIG GQG+A+A+ER
Sbjct: 359 GMSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIER 399


Lambda     K      H
   0.317    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: 428
Number of extensions: 20
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: 393
Length of database: 400
Length adjustment: 31
Effective length of query: 362
Effective length of database: 369
Effective search space:   133578
Effective search space used:   133578
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 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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