Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 353982 BT4456 putative electron transport protein (NCBI ptt file)
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__Btheta:353982 Length = 461 Score = 445 bits (1144), Expect = e-129 Identities = 225/452 (49%), Positives = 300/452 (66%), Gaps = 3/452 (0%) Query: 12 SQVHAYKADIFCRDETRVDWHSKALWLLREKRDRAAGSLPEWEQLRQLGSEIKLHTLTNL 71 S H+ A+ F +D WH++ LW++R KRD+ + +PEWE+LR E+KL++ ++L Sbjct: 2 STKHSKAAEKFLQDSKMAAWHNETLWMVRAKRDKMSKEVPEWEELRNKACELKLYSNSHL 61 Query: 72 AQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSMLTEECHLNPYL 131 + L+ FE+N ANG VHWAKD E+ IV+EIL H V +KSKSML EEC LNP+L Sbjct: 62 EELLQEFEKNATANGAIVHWAKDADEYCAIVYEILNEHNVHHFIKSKSMLAEECGLNPFL 121 Query: 132 EQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGTKAGESDPLYLT 191 +RGI+V+++DLGERI+QL + PSHIV+PAIH+K+E+VG+LF ++GT+ G DP YLT Sbjct: 122 MERGIDVVESDLGERILQLMHLEPSHIVLPAIHIKREQVGELFEKEMGTEKGNFDPTYLT 181 Query: 192 RAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMGIDKVV 251 AAR +LR FL+A+AAMTG N A+A G +VVCTNEGNADMG + PKL + + G++K+V Sbjct: 182 HAARKNLRHLFLNAEAAMTGANFAVASTGDIVVCTNEGNADMGTSYPKLNIAAFGMEKIV 241 Query: 252 PDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGEMHVIIVDNGRTEMMKDKILAESL 311 PD+D+ V R LAR+ATGQPVTTY++ YR P+ GE H+IIVDNGR+ ++ ++L Sbjct: 242 PDLDALGVFTRLLARSATGQPVTTYTSHYRRPREGGEYHIIIVDNGRSTILSKPDHIKTL 301 Query: 312 KCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATHDNTN--SIAWACTLCGSCTYV 369 CIRCG C+NTCPVYRRSGGYSY Y IPGPIGI +G HD AC+LC SC+ V Sbjct: 302 NCIRCGACMNTCPVYRRSGGYSYTYFIPGPIGINLGMAHDPEKYYDNLSACSLCMSCSDV 361 Query: 370 CPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMASTTLLNCSMGAARTALRILP 429 CP KV L + I+ R+ GK GK + M L N ++ AA + LP Sbjct: 362 CPVKVDLAEQIYKWRQDLDGLGKANTGKKIMSGGMKFLMERPALFNAALWAA-PMVNGLP 420 Query: 430 GSLLKPFSGAWGKYRELPVAPNSSFEAWFKKH 461 + WGK RELP SF +KK+ Sbjct: 421 RFMKYNDFDDWGKGRELPEFAKESFNEMWKKN 452 Lambda K H 0.320 0.134 0.413 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: 596 Number of extensions: 19 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: 464 Length of database: 461 Length adjustment: 33 Effective length of query: 431 Effective length of database: 428 Effective search space: 184468 Effective search space used: 184468 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: 51 (24.3 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