GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011385133.1
          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 (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