Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate RR42_RS30510 RR42_RS30510 maleylacetoacetate isomerase
Query= reanno::acidovorax_3H11:Ac3H11_2306 (222 letters) >FitnessBrowser__Cup4G11:RR42_RS30510 Length = 214 Score = 211 bits (538), Expect = 6e-60 Identities = 111/222 (50%), Positives = 140/222 (63%), Gaps = 9/222 (4%) Query: 1 MQLYNYFRSSASFRVRIALQIKGLAYDYLPVHLVKGEHKAPEYASRIGDALVPTLVTDGG 60 MQ+Y++F SS S+RVRIAL +KGL DY PV++ GEH+A +Y + I + V + DG Sbjct: 1 MQIYSFFNSSTSYRVRIALALKGLPCDYQPVNIRVGEHRAADYVAAINPSAVVPALVDGD 60 Query: 61 TALSQSMAIIEYLDETHPTPALLPATPLARARVRALAQMVACEIHPINNLRVLKYLVRDL 120 L QSMAII+YLD HP P L+P RARV LA ++AC+IHP+NN+R+L+YL L Sbjct: 61 FHLGQSMAIIDYLDACHPEPRLIPQAAEPRARVLELANVIACDIHPVNNMRILRYLQDTL 120 Query: 121 KVDEDAKNAWYRHWVRSGLEAFERQFALLAQERAAQGLAPSVLCWGDTPTLADCCLVPQI 180 V + K+AWY+HWV GL A ER LLAQ G P C+GD PTLADCCLVPQI Sbjct: 121 GVTPEQKDAWYQHWVDEGLGAVER---LLAQ----HGRGP--WCFGDQPTLADCCLVPQI 171 Query: 181 FNGQRFNVNLDGLPLTMGAFEACMALPAFQQAQPSACPDFEA 222 N QR + TM + PAFQQA+P PD+ A Sbjct: 172 ANAQRMGCRTERFERTMAVYRHACEHPAFQQAEPQRQPDYTA 213 Lambda K H 0.323 0.136 0.421 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: 179 Number of extensions: 4 Number of successful extensions: 2 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: 222 Length of database: 214 Length adjustment: 22 Effective length of query: 200 Effective length of database: 192 Effective search space: 38400 Effective search space used: 38400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 45 (21.9 bits)
Align candidate RR42_RS30510 RR42_RS30510 (maleylacetoacetate isomerase)
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))
# 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/TIGR01262.hmm # target sequence database: /tmp/gapView.30430.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01262 [M=211] Accession: TIGR01262 Description: maiA: maleylacetoacetate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-81 258.2 0.0 3.1e-81 258.1 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS30510 RR42_RS30510 maleylacetoacetate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS30510 RR42_RS30510 maleylacetoacetate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.1 0.0 3.1e-81 3.1e-81 2 210 .. 3 211 .. 2 212 .. 0.97 Alignments for each domain: == domain 1 score: 258.1 bits; conditional E-value: 3.1e-81 TIGR01262 2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkdGeqkkeef.kalNPqelvPtLkidegevltqSlAi 69 +Ys+f+Ss+syRvRiaLaLkg+ ++pvn++ Ge++++++ +a+NP++ vP+L++++ l qS+Ai lcl|FitnessBrowser__Cup4G11:RR42_RS30510 3 IYSFFNSSTSYRVRIALALKGLPCDYQPVNIRV-GEHRAADYvAAINPSAVVPALVDGD-FHLGQSMAI 69 8********************************.9*9999873679************5.********* PP TIGR01262 70 ieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekG 138 i+yL+ +pep+L+p+ ++ rarv +la++iacdihP++N+r+l++l+++lgv +e+k++w++hw+++G lcl|FitnessBrowser__Cup4G11:RR42_RS30510 70 IDYLDACHPEPRLIPQAAEPRARVLELANVIACDIHPVNNMRILRYLQDTLGVTPEQKDAWYQHWVDEG 138 ********************************************************************* PP TIGR01262 139 laalEellk.ekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpen 206 l a+E+ll+ + +g +c+Gd++tlad+cLvpq++nA+r+++ +++ + ++ +++ e+pafq+a+p++ lcl|FitnessBrowser__Cup4G11:RR42_RS30510 139 LGAVERLLAqHGRGPWCFGDQPTLADCCLVPQIANAQRMGCRTERFERTMAVYRHACEHPAFQQAEPQR 207 ********97889******************************************************** PP TIGR01262 207 qpdt 210 qpd+ lcl|FitnessBrowser__Cup4G11:RR42_RS30510 208 QPDY 211 ***7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (214 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: 7.28 // [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