Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate HSERO_RS01815 HSERO_RS01815 gamma-glutamyl kinase
Query= BRENDA::Q941T1 (735 letters) >FitnessBrowser__HerbieS:HSERO_RS01815 Length = 372 Score = 157 bits (398), Expect = 7e-43 Identities = 122/373 (32%), Positives = 189/373 (50%), Gaps = 25/373 (6%) Query: 30 VKDVKRIIIKVGTAVVTGPNGRLAMGRLGALCEQVKQLNFEGYEVILVTSGAVGVGRQRL 89 ++ KR+IIKVG+++VT L + EQ+ QL G EV+LV+SGAV G QRL Sbjct: 5 IQRAKRLIIKVGSSLVTNDGKGLDANAIARWAEQIAQLRALGKEVVLVSSGAVAEGMQRL 64 Query: 90 KYRKLVNSSFADLQNPQMDMDGKACAAVGQSVLMAIYDTLFSQLDVTSSQLLVTDRDFMD 149 + K P +ACAAVGQ L IY+T F + D+ ++Q+L+T D D Sbjct: 65 GFEK----------RPTGIHHLQACAAVGQMGLAQIYETSFRKHDLHTAQVLLTHADLAD 114 Query: 150 PSFGNQLRETVNSLLDLKVIPVFNENDAISTRRQPYEDSSGIFWDNDSLARLLAQELKAD 209 R T+ +LL L V+PV NEND + T F DND+L L+A ++A+ Sbjct: 115 RERYLNARSTLFALLQLGVVPVINENDTVVTDEIK-------FGDNDTLGALVANLIEAE 167 Query: 210 LLIMLSDVEGLYSGPP-SDPQSKII-HTYVHEQHGKLISFGEKSRVGRGGMQAKVAAAFT 267 LI+L+D GL++ P DP + +I + +LI+ G + +GRGGM K+ AA Sbjct: 168 ALIILTDQPGLFTADPRKDPTATLISEARAGDPSLELIAGGTGTGIGRGGMLTKILAAKR 227 Query: 268 ASSKGIPVVIASGFAIDSIIKVMRGEKIGTLFHREANQWGCSKEATAREMAVAARDC--S 325 A++ G VIA G + ++ GE IGT + E Q K+ A + A R + Sbjct: 228 AATSGAHTVIAWGREEQVLTRLAAGEAIGTQLNAETAQLTARKQWMADHLKTAGRVVLDA 287 Query: 326 RHLQKLSSEERKKILLDIADALE--ANEDLITSENQADLDLAQDIGYDKSLVARMTIK-- 381 +QKLS E + + + + + D+IT ++ +A+ + S AR I+ Sbjct: 288 GAVQKLSLEGKSLLPIGVVEVSGEFGRGDVITCVDENGRAIARGMSNYNSSDARRIIRHP 347 Query: 382 PGKIKSLAGSIRE 394 +I+++ G + E Sbjct: 348 SSEIQAILGFVEE 360 Lambda K H 0.318 0.136 0.385 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: 563 Number of extensions: 30 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: 735 Length of database: 372 Length adjustment: 35 Effective length of query: 700 Effective length of database: 337 Effective search space: 235900 Effective search space used: 235900 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: 52 (24.6 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