Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate 352217 BT2690 histidine ammonia-lyase (NCBI ptt file)
Query= reanno::SB2B:6937475 (497 letters) >FitnessBrowser__Btheta:352217 Length = 499 Score = 405 bits (1042), Expect = e-117 Identities = 224/490 (45%), Positives = 312/490 (63%), Gaps = 4/490 (0%) Query: 3 FRYGVDHLTLETVNGIANGSIQAELCQQAIDKINASRHNVD-VMAASDKAIYGINTGFGP 61 ++ G LT E + I N +++ EL +A +I R +D +A+S++ +YGI TGFG Sbjct: 6 YQIGSGELTFEIIERIINENLKLELAPEAKLRIQKCRDYLDHKIASSEEPLYGITTGFGS 65 Query: 62 LCDTQISPAETHLLQKNLLITHAVGVGEPIAKSISKLMLITKVHALSQGFSGIRLDVVER 121 LC ISP E LQ+NL+ +HA VGE I I KLM++ K HALS G SG++L V+R Sbjct: 66 LCTKNISPGELGTLQENLIKSHACSVGEEIRPVIIKLMMLLKAHALSLGHSGVQLITVQR 125 Query: 122 MLAFIALDLIPVVPEQGSVGASGDLAPLSHLFLPLLGEGEFWQGDKIVPAREALKAHGLE 181 +L F D++P+V ++GS+GASGDLAPL++LFLPL+G G+ K A L G E Sbjct: 126 ILDFFNNDVLPIVYDRGSLGASGDLAPLANLFLPLIGVGDVNYKGKKCEAISVLDEFGWE 185 Query: 182 PLELHAKEGLALINGTQFILSHAITALTKMGYLLDLADLAGAMSIEGMQGSQSPFRAELH 241 P+ L +KEGLAL+NGTQF+ ++ + A+ K L ADL A+S+E G PF + Sbjct: 186 PVRLMSKEGLALLNGTQFMSANGVFAILKAFRLSKKADLIAALSLEAFDGRIDPFMDCIQ 245 Query: 242 EIRPFAGNIEVAARMRSFFKDSENMASHEDCDRVQDPYSLRCIPQVHGASRNAYNHLKEL 301 +IRP G IE R SE + + VQDPYS RCIPQVHGA+++A ++ + Sbjct: 246 QIRPHPGQIETGEAFRKLLAGSELIERPK--AHVQDPYSFRCIPQVHGATKDAIRYVSSV 303 Query: 302 AEIEMNSVTDNPIVISAEE-AISGGGFHGQPLAMVLDYTSIAAAELGNISDRRCYLLLEG 360 E+NSVTDNP + E+ ISGG FHGQPLA+ D+ +IA AELGNIS+RR L+ G Sbjct: 304 LLTEINSVTDNPTIFPDEDRIISGGNFHGQPLAISYDFLAIALAELGNISERRVSQLIMG 363 Query: 361 LHGLPRLLTTSGGLNSGMMIPQYVTAALVTENKSLCFPPSADSVPTSMGQEDHVSMGSIS 420 L LP L + GLNSG MIPQY A++V++NK C+ S+DS+ +S GQEDHVSMG+ + Sbjct: 364 LRELPEFLVANPGLNSGFMIPQYAAASMVSQNKMYCYAASSDSIVSSNGQEDHVSMGANA 423 Query: 421 GRKLNQILGNLEKIFAIELMYAAQAIDFRRPNRCSDIIEQNHALIREKVAKLEEDRLLKP 480 KL +++ NLE I AIELM AAQ IDFRRP + S ++E R++V +++D ++ Sbjct: 424 ATKLYKVMDNLEHILAIELMNAAQGIDFRRPLKTSPLLESFLHAYRKEVPFVKDDIVMYK 483 Query: 481 DIDAIIALVK 490 +I +A +K Sbjct: 484 EIHKTVAFLK 493 Lambda K H 0.319 0.136 0.387 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: 586 Number of extensions: 25 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: 497 Length of database: 499 Length adjustment: 34 Effective length of query: 463 Effective length of database: 465 Effective search space: 215295 Effective search space used: 215295 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 (21.8 bits) S2: 52 (24.6 bits)
Align candidate 352217 BT2690 (histidine ammonia-lyase (NCBI ptt file))
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))
# 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/TIGR01225.hmm # target sequence database: /tmp/gapView.8933.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01225 [M=506] Accession: TIGR01225 Description: hutH: histidine ammonia-lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-177 577.5 0.0 1.2e-177 577.4 0.0 1.0 1 lcl|FitnessBrowser__Btheta:352217 BT2690 histidine ammonia-lyase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:352217 BT2690 histidine ammonia-lyase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 577.4 0.0 1.2e-177 1.2e-177 3 494 .. 8 497 .. 6 499 .] 0.98 Alignments for each domain: == domain 1 score: 577.4 bits; conditional E-value: 1.2e-177 TIGR01225 3 ldgesltledleavarekarvelsaaaeeavaksravie.eivaedktvYGvntGFGklasvkidkedlaeLqrnl 77 + +++lt e +e++ e+ ++el+ +a+ +++k r ++ +i+++++++YG++tGFG+l +i +l +Lq+nl lcl|FitnessBrowser__Btheta:352217 8 IGSGELTFEIIERIINENLKLELAPEAKLRIQKCRDYLDhKIASSEEPLYGITTGFGSLCTKNISPGELGTLQENL 83 667899*******************************983688899****************************** PP TIGR01225 78 vrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGasGDLAPLahlalv 153 ++sHa+ vGe++ +++++++l++++l+ G+sgv+ +++ +++++n++vlP+v ++Gs+GasGDLAPLa l l lcl|FitnessBrowser__Btheta:352217 84 IKSHACSVGEEIRPVIIKLMMLLKAHALSLGHSGVQLITVQRILDFFNNDVLPIVYDRGSLGASGDLAPLANLFLP 159 **************************************************************************** PP TIGR01225 154 liGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdaekllesadiaaalsleallg 229 liG G+++++g+ +a ++L++ g ePv+l +kEGlAL+nGtq+m+a +v a+ +a +l ++ad++aalslea g lcl|FitnessBrowser__Btheta:352217 160 LIGVGDVNYKGKKCEAISVLDEFGWEPVRLMSKEGLALLNGTQFMSANGVFAILKAFRLSKKADLIAALSLEAFDG 235 **************************************************************************** PP TIGR01225 230 tskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslRciPqvhGavldtldqvkevlaiEln 305 ++f + i+++rph+gqi++++++r+llagse+ e+ + +vqD+Ys RciPqvhGa++d++++v +vl +E+n lcl|FitnessBrowser__Btheta:352217 236 RIDPFMDCIQQIRPHPGQIETGEAFRKLLAGSELIERP--KAHVQDPYSFRCIPQVHGATKDAIRYVSSVLLTEIN 309 ***********************************998..899********************************* PP TIGR01225 306 satDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaiseRRierlldpalseLppFLaedsGlnsGlmia 381 s+tDnP +f+de++++sgGnFHg+p+A+ dflaia+aelg+iseRR+++l+ l eLp FL++++GlnsG+mi+ lcl|FitnessBrowser__Btheta:352217 310 SVTDNPTIFPDEDRIISGGNFHGQPLAISYDFLAIALAELGNISERRVSQLIM-GLRELPEFLVANPGLNSGFMIP 384 ***************************************************96.6889****************** PP TIGR01225 382 qytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaaarkllevvenvrrviaiEllaaaqglefrkaektaae 457 qy+aA++vs+nk ++ as Dsi +s qEDHvsmga aa kl++v++n+++++aiEl+ aaqg++fr++ kt++ lcl|FitnessBrowser__Btheta:352217 385 QYAAASMVSQNKMYCYAASSDSIVSSNGQEDHVSMGANAATKLYKVMDNLEHILAIELMNAAQGIDFRRPLKTSPL 460 **************************************************************************** PP TIGR01225 458 lekvyeavRevveeleeDRvlapDleavkellekesl 494 le +a R++v+ +++D v+ +++++ +l++ +l lcl|FitnessBrowser__Btheta:352217 461 LESFLHAYRKEVPFVKDDIVMYKEIHKTVAFLKRTKL 497 *****************************99998877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (506 nodes) Target sequences: 1 (499 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9.16 // [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