GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Ammonifex degensii KC4

Align Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13 (uncharacterized)
to candidate WP_015739819.1 ADEG_RS09385 fructose 1,6-bisphosphatase

Query= curated2:B6YTP6
         (375 letters)



>NCBI__GCF_000024605.1:WP_015739819.1
          Length = 376

 Score =  472 bits (1214), Expect = e-138
 Identities = 229/369 (62%), Positives = 286/369 (77%), Gaps = 9/369 (2%)

Query: 6   KITISVIKADIGGWPGHSRVHPQLIEAAEEVLAKAKEEGTIIDFYVAYAGDDLQLIMTHK 65
           K+T+SVIKADIGG+ GHS VHP++ E A   L K      +ID+YVA+ GDDL LIMTH+
Sbjct: 3   KVTLSVIKADIGGFVGHSAVHPEVKEKARACLEK---HPLLIDYYVAHVGDDLVLIMTHE 59

Query: 66  KGVDSPDIHGLAWKAFEEATEIAKEFGLYGAGQDLLKDAFSGNIRGMGPGIAEMEITLRK 125
            G +  +IH LAW  F   TE+AK+  LYGAGQDLL DAFSGN++G+GPG+AEME+  R+
Sbjct: 60  HGRNKGEIHKLAWDTFVACTEVAKKLKLYGAGQDLLADAFSGNVKGLGPGVAEMEVEERE 119

Query: 126 SEPIVTFHMDKTEPGAFNLPIFRMFADPFNTAGLVIDPNMHMGFRFEVWDIKEHKRVILN 185
           SEP+V    DKTEPGA+NLP++++FADPFNT GL+IDP MH GF FEV D+ E K++I N
Sbjct: 120 SEPVVVLMADKTEPGAWNLPLYKIFADPFNTIGLIIDPKMHCGFAFEVRDLIEDKKIIFN 179

Query: 186 TPEEIYDLLALIGAKSRYVIKRVYPKEGHKISKDEPVAVISTEKLYEIAGEYVGKDDPVA 245
            PE++YD+L  IGA  RY IKRV+ +        E  AV ST++L  +AG YVGKDDPV 
Sbjct: 180 APEDLYDMLVFIGAPGRYAIKRVFHR-----GTGEIAAVSSTQRLNLMAGRYVGKDDPVC 234

Query: 246 IVRAQSGLPALGEVLEPFAFPHLVSGWMRGSHNGPIMPVPMHQANPTRFDGPPRVVALGW 305
           IVR Q+G P++GEVLEPFAFPHLVSGWMRGSH+GP+MPV M  A PTRFDGPPRVVALG+
Sbjct: 235 IVRCQNGYPSVGEVLEPFAFPHLVSGWMRGSHSGPLMPVSMDDARPTRFDGPPRVVALGF 294

Query: 306 QISPEGKLVGPVDLFDDPAFDYARQKALEITEYIRRHGPFEPHRLPLEDMEYTTLPGVLK 365
           Q++ +GKL+GP D F DPAFD AR+ ALEI +Y+RR GPFEPHRL L++MEYTT+P V++
Sbjct: 295 QLA-DGKLIGPNDFFSDPAFDNARRLALEIADYLRRLGPFEPHRLHLDEMEYTTMPQVME 353

Query: 366 KLEERFEDI 374
           KL +RF D+
Sbjct: 354 KLRDRFIDL 362


Lambda     K      H
   0.319    0.140    0.425 

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: 547
Number of extensions: 19
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: 375
Length of database: 376
Length adjustment: 30
Effective length of query: 345
Effective length of database: 346
Effective search space:   119370
Effective search space used:   119370
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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