Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 353982 BT4456 putative electron transport protein (NCBI ptt file)
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Btheta:353982 Length = 461 Score = 233 bits (594), Expect = 2e-65 Identities = 153/441 (34%), Positives = 230/441 (52%), Gaps = 32/441 (7%) Query: 35 RASRANAFKDIDE-KAIIAEVADAKDHAAKNMDTLYAQFKAEAEKRGVKVHLARTAAEAN 93 RA R K++ E + + + + K ++ +++ L +F+ A G VH A+ A E Sbjct: 30 RAKRDKMSKEVPEWEELRNKACELKLYSNSHLEELLQEFEKNATANGAIVHWAKDADEYC 89 Query: 94 EIIARIARDNNCKKAIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMV 153 I+ I ++N IKSKSM AEE LN L E ++V+E+DLGE I+Q+ H PSH+V Sbjct: 90 AIVYEILNEHNVHHFIKSKSMLAEECGLNPFLMERGIDVVESDLGERILQLMHLEPSHIV 149 Query: 154 MPAIHLSRYQVADLF-SEVTKQKQEVDIQRLVKVARRELRTHFATADMGISGANFAVAET 212 +PAIH+ R QV +LF E+ +K D L AR+ LR F A+ ++GANFAVA T Sbjct: 150 LPAIHIKREQVGELFEKEMGTEKGNFDPTYLTHAARKNLRHLFLNAEAAMTGANFAVAST 209 Query: 213 GTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTW 272 G I + TNEGNA + T+ P++++A G++K+VP L ++L R+ATGQ +T+Y + Sbjct: 210 GDIVVCTNEGNADMGTSYPKLNIAAFGMEKIVPDLDALGVFTRLLARSATGQPVTTYTSH 269 Query: 273 IGGANECEACVDGRKEMHIVFLDNGRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGH 332 E E HI+ +DNGR + P + L C+RCGAC N CPVYR GG+ Sbjct: 270 YRRPRE-------GGEYHIIIVDNGRSTILSKPDHIKTLNCIRCGACMNTCPVYRRSGGY 322 Query: 333 KMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCESCKHICAGGIDLPRLIKEIRARLN- 391 + G IG+ L H +K + + C C SC +C +DL I + R L+ Sbjct: 323 SYTYFIPGPIGINLG-MAHDPEKYYDNLSACSLCMSCSDVCPVKVDLAEQIYKWRQDLDG 381 Query: 392 ---EEEGMPVETTLMGKMLKNRKLFHTLLRFAKWAQKPVTGGTPYIRHLPQIFAKDHGF- 447 G + + M +++ LF+ L WA P + LP+ F K + F Sbjct: 382 LGKANTGKKIMSGGMKFLMERPALFNAAL----WA-------APMVNGLPR-FMKYNDFD 429 Query: 448 -----KALPAIADKPFRDEWE 463 + LP A + F + W+ Sbjct: 430 DWGKGRELPEFAKESFNEMWK 450 Lambda K H 0.321 0.135 0.402 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: 781 Number of extensions: 37 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 717 Length of database: 461 Length adjustment: 36 Effective length of query: 681 Effective length of database: 425 Effective search space: 289425 Effective search space used: 289425 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 (21.9 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