Align glutaminyl-tRNA synthase (glutamine-hydrolysing) (EC 6.3.5.7) (characterized)
to candidate Pf1N1B4_4382 N-carbamoylputrescine amidase (EC 3.5.1.53)
Query= BRENDA::Q9H0R6 (528 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4382 Length = 571 Score = 120 bits (300), Expect = 2e-31 Identities = 106/362 (29%), Positives = 158/362 (43%), Gaps = 68/362 (18%) Query: 5 SLREVSAALKQGQITPTELCQKCLSLIKK------TKFLNAYITVSEEVALKQAEESEKR 58 S+ ++ AAL+ GQ T EL Q L+ I LNA + V ALK+A+ S+ R Sbjct: 8 SIAQLRAALESGQTTAVELVQAYLARIDAYDGPDTPTALNA-VVVRNPDALKEAQASDAR 66 Query: 59 YKNGQSLGDLDGIPIAVKDNFSTSGIETTCASNMLKGYIPPYNATVVQKLLDQGALLMGK 118 G+SLG LDGIP KD++ G+ S I +A +++L GA+ +GK Sbjct: 67 RARGESLGPLDGIPYTAKDSYLVKGLTAASGSPAFANLIAYRDAFTIERLRAAGAICLGK 126 Query: 119 TNLDEFAMGSGSTDGVFGPVKNPWSYSKQYREKRKQNPHSENEDSDWL---ITGGSSGGS 175 TN+ A G G GV+G ++P++ +D+L GSS G+ Sbjct: 127 TNMPPMANG-GMQRGVYGRAESPYN-------------------ADYLTAPFASGSSNGA 166 Query: 176 AAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFKPSYGLVSRHGLIPLVNSMDVPGILTR 235 A +A L +T S R PA++ GL + PS G++S G PL +MDV R Sbjct: 167 GTATAASFAAFGLAEETWSSGRGPASNNGLCAYTPSRGVISVRGNWPLTPTMDVVVPFAR 226 Query: 236 CVDDAAIVLGALAGPDPRDSTTVHEPINKPFM-LPSLADVSKLC---------------I 279 + D VL + DP + +P++ +PS+A V + Sbjct: 227 TMADLLEVLDVVVADDPDTRGDLWRM--QPWVPIPSVASVRPASYGSLAANTDALAGKRL 284 Query: 280 GIPKEYLV--PELSSE------------------VQSLWSKAADLFESEGAKVIEVSLPH 319 G+P+ Y+ PE + V LW +A E+ GA+VIEV P Sbjct: 285 GVPRMYINADPEAGTSDAPGIGGPTGQRINTRPSVIGLWEEARKALEAFGAEVIEVDFPL 344 Query: 320 TS 321 S Sbjct: 345 VS 346 Score = 42.0 bits (97), Expect = 6e-08 Identities = 30/106 (28%), Positives = 53/106 (50%), Gaps = 12/106 (11%) Query: 397 QKVRRLIANDFVNAFNSGVDVLLTPTTL------SEAVPYLEFIKEDNRTRSAQDDIFTQ 450 ++ RR+ D+++ G+D ++ PT ++ P I N A ++ Sbjct: 451 EQTRRIDLEDWMDRL--GLDAVIFPTVADVGPANADVDPKSADIAWSNGVWVANGNL--- 505 Query: 451 AVNMAGLPAVSIPVALSNQ-GLPIGLQFIGRAFCDQQLLTVAKWFE 495 A+ G+P V++P+ + G+P+GL F GRA+ D LL +A FE Sbjct: 506 AIRHLGVPTVTVPMGIMPDIGMPVGLTFAGRAYDDSTLLRLASAFE 551 Lambda K H 0.317 0.133 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: 639 Number of extensions: 32 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 528 Length of database: 571 Length adjustment: 36 Effective length of query: 492 Effective length of database: 535 Effective search space: 263220 Effective search space used: 263220 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 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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