Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate 3610097 Dshi_3478 4-carboxymuconolactone decarboxylase (RefSeq)
Query= BRENDA::Q6SJA7 (118 letters) >FitnessBrowser__Dino:3610097 Length = 128 Score = 200 bits (508), Expect = 6e-57 Identities = 99/116 (85%), Positives = 106/116 (91%) Query: 1 MTTRRAVLGDAHVDRAEAAKTELDAPFQSLITEAAWGTVWASDKISRRERSMLTLALLAA 60 M RRAVLGDAHVDRAEAAK LDAPFQSLITEAAWGTVWASD ISRRERSMLTLALLAA Sbjct: 11 MEVRRAVLGDAHVDRAEAAKNPLDAPFQSLITEAAWGTVWASDAISRRERSMLTLALLAA 70 Query: 61 TGNFEEIPMHIRATANTGASKSDVIEAFQHVAIYAGVPKANHALKLAKQTYQEMEA 116 TGNF+EIPMH+RA NTGASK+DV+E FQHVAIYAGVP+ANHA+KLAK T+ EMEA Sbjct: 71 TGNFDEIPMHVRACVNTGASKTDVMEVFQHVAIYAGVPRANHAIKLAKATFAEMEA 126 Lambda K H 0.315 0.125 0.348 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: 113 Number of extensions: 1 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: 118 Length of database: 128 Length adjustment: 14 Effective length of query: 104 Effective length of database: 114 Effective search space: 11856 Effective search space used: 11856 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 (21.7 bits) S2: 41 (20.4 bits)
Align candidate 3610097 Dshi_3478 (4-carboxymuconolactone decarboxylase (RefSeq))
to HMM TIGR02425 (pcaC: 4-carboxymuconolactone decarboxylase (EC 4.1.1.44))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02425.hmm # target sequence database: /tmp/gapView.5585.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02425 [M=123] Accession: TIGR02425 Description: decarb_PcaC: 4-carboxymuconolactone decarboxylase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-60 188.3 0.5 2.7e-60 188.1 0.5 1.0 1 lcl|FitnessBrowser__Dino:3610097 Dshi_3478 4-carboxymuconolactone Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3610097 Dshi_3478 4-carboxymuconolactone decarboxylase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 188.1 0.5 2.7e-60 2.7e-60 2 122 .. 4 124 .. 3 125 .. 0.98 Alignments for each domain: == domain 1 score: 188.1 bits; conditional E-value: 2.7e-60 TIGR02425 2 keryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgreeelalh 78 k rye G++vrravlGdahvdra+aak+ +da+fq+liteaaWGtvWa+d +s+rers++t+allaa+g+ +e+ +h lcl|FitnessBrowser__Dino:3610097 4 KSRYEIGMEVRRAVLGDAHVDRAEAAKNPLDAPFQSLITEAAWGTVWASDAISRRERSMLTLALLAATGNFDEIPMH 80 689************************************************************************** PP TIGR02425 79 vraaantGvteddikevllqvaiyaGvPaankalklakevlael 122 vra++ntG+++ d+ ev+++vaiyaGvP+an+a+klak ++ae+ lcl|FitnessBrowser__Dino:3610097 81 VRACVNTGASKTDVMEVFQHVAIYAGVPRANHAIKLAKATFAEM 124 ******************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (123 nodes) Target sequences: 1 (128 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 5.14 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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