Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS17580 Length = 440 Score = 197 bits (500), Expect = 7e-55 Identities = 137/415 (33%), Positives = 204/415 (49%), Gaps = 49/415 (11%) Query: 26 VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGK--FWHTGNGYTNEPV 83 V GEG L DQ GK YID +GG AV+ LGH HPR+++A+ +Q G+ + HT + +T P Sbjct: 17 VAGEGMELIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELAYAHT-SFFTTAPA 75 Query: 84 LRLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGR 141 LA L DA + V+F + G+EA EAALKLAR+Y + ++ I+A + ++HG Sbjct: 76 EELAAMLADAAPGSLNHVYFLSGGSEAVEAALKLARQYYVEVGQPQRRHIIARRQSYHGN 135 Query: 142 TLFTVSAGGQPAYSQDFAPLPPQIQHAI-----------YNDLDSAKALID--------- 181 TL ++ GG + F P+ + H +D+ + L D Sbjct: 136 TLGALAIGGNAWRREMFMPMLIEAHHVSPCYAYRNRADGESDVQYVQRLADELEQKILSL 195 Query: 182 --DNTCAVIVEPMQGE-GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAY 238 D A + E + G G VP D+ R +R +CD + LLI DEV +G+GRTG L+A Sbjct: 196 GADQVIAFVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVMSGMGRTGYLFAC 255 Query: 239 MHYGVTPDLLSTAKALGGGF-PIGALLASERCASVMTVGT----HGTTYGGNPLACAVAG 293 GV PD++ AK LG G+ PIGA++ S+ + G+ HG TY G+ ACA A Sbjct: 256 EEDGVVPDIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGSGFFQHGHTYIGHATACAAAV 315 Query: 294 EVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKA-- 351 V TI +L V+QR + L +IRG GL +G L E + K Sbjct: 316 AVQKTIQEERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGVELVAERSSKLPL 375 Query: 352 -------KAISNQAAEEGLMILIAGANV-------VRFAPALIISEDEVNSGLDR 392 + +A + GL++ G + + AP I S ++++ + R Sbjct: 376 SPDLRTHARVKAEAMKRGLLVYPMGGTIDGKNGDHILLAPPFIASSNDISEIVQR 430 Lambda K H 0.321 0.137 0.412 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: 434 Number of extensions: 28 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: 406 Length of database: 440 Length adjustment: 32 Effective length of query: 374 Effective length of database: 408 Effective search space: 152592 Effective search space used: 152592 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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