Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate 353982 BT4456 putative electron transport protein (NCBI ptt file)
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__Btheta:353982 Length = 461 Score = 285 bits (730), Expect = 2e-81 Identities = 168/461 (36%), Positives = 253/461 (54%), Gaps = 29/461 (6%) Query: 18 AEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALSRLPDLLEQL 77 AE+ L D ++ + + KR + E E LR +K + S L +LL++ Sbjct: 9 AEKFLQDSKMAAWHNETLWMVRAKRDKMSKEVPEWEELRNKACELKLYSNSHLEELLQEF 68 Query: 78 EQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAERGVEC 137 E+ T NG VHWA+ +E ++V+ I+ +K KSM++EE +N +L ERG++ Sbjct: 69 EKNATANGAIVHWAKDADEYCAIVYEILNEHNVHHFIKSKSMLAEECGLNPFLMERGIDV 128 Query: 138 LESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLG-EPETEDVNQLIQIGRRTL 196 +ESD+GE I+QL + +PSHI++PAIH QV +LF ++G E D L R+ L Sbjct: 129 VESDLGERILQLMHLEPSHIVLPAIHIKREQVGELFEKEMGTEKGNFDPTYLTHAARKNL 188 Query: 197 RRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPNLRDVV 256 R F+ A+ ++G NFA+A TG +++ NEGN M T+ P ++IA G+EK+VP+L + Sbjct: 189 RHLFLNAEAAMTGANFAVASTGDIVVCTNEGNADMGTSYPKLNIAAFGMEKIVPDLDALG 248 Query: 257 PLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFADAQMRQTLN 316 LL RSA GQP+TTY + PR+ E H++++DNGR+ + +TLN Sbjct: 249 VFTRLLARSATGQPVTTYTSHYRRPREGG------EYHIIIVDNGRSTILSKPDHIKTLN 302 Query: 317 CIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMA-GLDKVPDHPSASSLCGACGE 375 CIRCGACMN CPVY R GG++Y PGPIG I MA +K D+ SA SLC +C + Sbjct: 303 CIRCGACMNTCPVYRRSGGYSYTYFIPGPIG--INLGMAHDPEKYYDNLSACSLCMSCSD 360 Query: 376 VCPVKIPIPELLQRLRQ--ENVKNPEQPQQVKGGGAKYSRTERWIWRGWQMLNTRPALYR 433 VCPVK+ + E + + RQ + + +++ GG K+ L RPAL+ Sbjct: 361 VCPVKVDLAEQIYKWRQDLDGLGKANTGKKIMSGGMKF-------------LMERPALFN 407 Query: 434 SFLWAATRF----RALAPKKAGPWTENHSAPVPARRSLHDL 470 + LWAA R + W + P A+ S +++ Sbjct: 408 AALWAAPMVNGLPRFMKYNDFDDWGKGRELPEFAKESFNEM 448 Lambda K H 0.317 0.135 0.403 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: 565 Number of extensions: 25 Number of successful extensions: 6 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: 483 Length of database: 461 Length adjustment: 33 Effective length of query: 450 Effective length of database: 428 Effective search space: 192600 Effective search space used: 192600 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: 51 (24.3 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