Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_015945416.1 DHAF_RS23525 triose-phosphate isomerase
Query= BRENDA::Q6GIL6 (253 letters) >NCBI__GCF_000021925.1:WP_015945416.1 Length = 255 Score = 250 bits (638), Expect = 2e-71 Identities = 130/252 (51%), Positives = 174/252 (69%), Gaps = 5/252 (1%) Query: 2 RTPIIAGNWKMNKTVQEAKDF-VNALPTLPDSKEVESVICAPAIQLDALTTAVKEGKAQG 60 R PIIAGNWKMNK+++E +++ V L L + ++ V+CAP L+ L ++E Sbjct: 4 RHPIIAGNWKMNKSLRETQEYAVKLLGVLGEVTAIDVVVCAPFTALNVLKNELEESV--- 60 Query: 61 LEIGAQNTYFEDNGAFTGETSPVALADLGVKYVVIGHSERRELFHETDEEINKKAHAIFK 120 + IGAQ+ ++ +GA+TGE S L D+ YV++GHSERRE+ ETDEEI KK A K Sbjct: 61 IHIGAQDMFYAPDGAYTGEISAAMLVDVACTYVILGHSERREILRETDEEIAKKVKAALK 120 Query: 121 HGMTPIICVGETDEERESGKANDVVGEQVKKAVAGLSEDQLKSVVIAYEPIWAIGTGKSS 180 G+TPI+CVGE RE GKA +V QV+K + L+ D LK VVIAYEPIWAIGTGK++ Sbjct: 121 AGLTPILCVGENLANREEGKAFAIVRGQVEKDLTDLAPDDLKRVVIAYEPIWAIGTGKTA 180 Query: 181 TSEDANEMCAFVRQTIADLSSKEVSEATRIQYGGSVKPNNIKEYMAQTDIDGALVGGASL 240 +SEDA EMCA +R T+A ++ V++ I YGGSVK +NI E M+Q D+DGALVGGASL Sbjct: 181 SSEDAQEMCAMIRSTLAGIAG-VVADEVNILYGGSVKADNIGELMSQPDVDGALVGGASL 239 Query: 241 KVEDFVQLLEGA 252 + E F QL++ A Sbjct: 240 EAEGFAQLVQNA 251 Lambda K H 0.311 0.129 0.359 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: 205 Number of extensions: 8 Number of successful extensions: 3 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: 253 Length of database: 255 Length adjustment: 24 Effective length of query: 229 Effective length of database: 231 Effective search space: 52899 Effective search space used: 52899 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_015945416.1 DHAF_RS23525 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))
# 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/TIGR00419.hmm # target sequence database: /tmp/gapView.4028450.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00419 [M=228] Accession: TIGR00419 Description: tim: triose-phosphate isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-64 204.2 2.9 1.4e-64 204.0 2.9 1.0 1 NCBI__GCF_000021925.1:WP_015945416.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000021925.1:WP_015945416.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 204.0 2.9 1.4e-64 1.4e-64 1 228 [] 7 242 .. 7 242 .. 0.93 Alignments for each domain: == domain 1 score: 204.0 bits; conditional E-value: 1.4e-64 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 ++ +n+K+n s+ + ++ kl + +++ + v+v pf l+v+k+e+e s i+++Aq++ Ga+tGe NCBI__GCF_000021925.1:WP_015945416.1 7 IIAGNWKMNKSLRETQEYAVKLLGVLGEVTAIDVVVCAPFTALNVLKNELEeSVIHIGAQDMFYAPDGAYTGE 79 689***********************************************9999******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145 isA+ml+d+ + +v++gHsErR +l+e+de i+kkv + + gl++++Cvge l++re ++ + v + + NCBI__GCF_000021925.1:WP_015945416.1 80 ISAAMLVDVACTYVILGHSERREILRETDEEIAKKVKAALKAGLTPILCVGENLANREEGKAFAIVRGQVEKD 152 **********************************************************666665554432221 PP TIGR00419 146 A.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211 l+ +v+A+EP+++iGtGk++s +a+++ +++r l+ ++ va++v++lyG+sv+a + el+ NCBI__GCF_000021925.1:WP_015945416.1 153 LtdlapddLKRVVIAYEPIWAIGTGKTASSEDAQEMCAMIRSTLAGIAGVVADEVNILYGGSVKADNIGELMS 225 11333677***************************************************************** PP TIGR00419 212 qldvdGvLlasavlkae 228 q+dvdG+L+++a+l ae NCBI__GCF_000021925.1:WP_015945416.1 226 QPDVDGALVGGASLEAE 242 **************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (255 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 13.70 // [ok]
This GapMind analysis is from Sep 24 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