Align histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate 6939292 Sama_3385 histidine ammonia-lyase (RefSeq)
Query= BRENDA::P42357 (657 letters) >FitnessBrowser__SB2B:6939292 Length = 518 Score = 282 bits (721), Expect = 3e-80 Identities = 172/462 (37%), Positives = 263/462 (56%), Gaps = 14/462 (3%) Query: 109 EPEKYIELDGDRLTTEDLVNLGKG-RYKIKLTPTAEKRVQKSREVIDSIIKEKTVVYGIT 167 E ++ ++ LT E +V + KG R +++ + +Q+ IDS++ E+ VVYG+T Sbjct: 7 EMKETVKFGYGALTIEQVVAIAKGARVELRRDQEYVEYIQRGARFIDSLLAEEGVVYGVT 66 Query: 168 TGFGKFARTVIPINKLQELQVNLVRSHSSGVGKPLSPERCRMLLALRINVLAKGYSGISL 227 TG+G + ++ + EL ++L R H G+G+ L+P + R ++A R+N LA G SG+S Sbjct: 67 TGYGDSCTVTVGLDLVHELPLHLSRFHGCGMGRELTPMQSRAVMACRLNSLAIGKSGVSF 126 Query: 228 ETLKQVIEMFNASCLPYVPEKGTVGASGDLAPLSHLALGLVGEGKMWSPKSGWADAKYVL 287 E L+++ + N P +PE+G+VGASGDL PLS+LA L+GE ++ + G + V Sbjct: 127 ELLERIETLINEDICPVIPEEGSVGASGDLTPLSYLAGVLIGERDVFY-RGGRLPSSEVF 185 Query: 288 EAHGLKPVILKPKEGLALINGTQMITSLGCEAVERASAIARQADIVAALTLEVLKGTTKA 347 + + P+ L+PKEGLAL+NGT ++T+L C A +RA + R + + A+ LKG + Sbjct: 186 QKLNITPLKLRPKEGLALMNGTAVMTALACLAYDRADYLTRLSSRITAMASLTLKGNSNH 245 Query: 348 FDTDIHALRPHRGQIEVAFRFRSLLDSDHHPSEIAESHRFCDRVQDAYTLRCCPQVHGVV 407 FD + A +PH GQ VA R L+ HP R DR+QD Y++RC P + GV+ Sbjct: 246 FDDILFAAKPHPGQSRVASWIRDDLNHHEHP-------RNSDRLQDRYSIRCAPHIIGVL 298 Query: 408 NDTIAFVKNIITTELNSATDNPMVFANRGETVSGGNFHGEYPAKALDYLAIGIHELAAIS 467 D ++ I ELNSA DNP+V + GG+F+G + A A+D L + ++ + Sbjct: 299 ADAQPMLRQFIENELNSANDNPIVDGEGEHILHGGHFYGGHIAFAMDSLKNLVANISDLI 358 Query: 468 ERRIERLCNPSLSE-LPAFLV-AEGG---LNSGFMIAHCTAAALVSENKALCHPSSVDSL 522 +R++ + +P + LPA L AEG +N GF +A +E L P+SV S Sbjct: 359 DRQMALVMDPKFNNGLPANLSGAEGARRPINHGFKAVQIGVSAWTAEALKLTMPASVFSR 418 Query: 523 STSAATEDHVSMGGWAARKALRVIEHVEQVLAIELLAACQGI 564 ST +D VSMG AAR LRV+E EQV A LLA QG+ Sbjct: 419 STECHNQDKVSMGTIAARDCLRVLELTEQVAAAALLAMTQGM 460 Lambda K H 0.319 0.135 0.398 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: 751 Number of extensions: 35 Number of successful extensions: 4 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: 657 Length of database: 518 Length adjustment: 36 Effective length of query: 621 Effective length of database: 482 Effective search space: 299322 Effective search space used: 299322 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: 53 (25.0 bits)
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