Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate WP_072909151.1 BUB13_RS12755 iron-sulfur cluster-binding protein
Query= uniprot:Q726S3 (717 letters) >NCBI__GCF_900142125.1:WP_072909151.1 Length = 679 Score = 290 bits (743), Expect = 1e-82 Identities = 177/484 (36%), Positives = 268/484 (55%), Gaps = 22/484 (4%) Query: 1 MQNSKTLKEYRKELQESLDNEFLRNAMDKFA---VAYRASRANAFKDIDEKAIIAEVADA 57 M+ + T +R ++ N+ ++ A+ A RA+ N + +E + Sbjct: 1 MKPTATRHNFRAASSSAIQNKRVQKAVRNTAGLLARMRATTVNTKPEFEELRNWGR--NR 58 Query: 58 KDHAAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAE 117 K ++N++ AQFKA+ E++G VH A+ AAEA II+ IAR+ A+KSKSMT+E Sbjct: 59 KLLVSENLEKWVAQFKAQVEQQGGVVHRAKDAAEAGRIISEIARERGITAAVKSKSMTSE 118 Query: 118 ETHLNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQE 177 E LN L++ + V ETDLGE+I+Q+ E PSH++ PAIH ++ V LF+E + Sbjct: 119 EVGLNDILQDAGITVTETDLGEFIVQLAGEHPSHILAPAIHRNQDDVRKLFTEKLGAPAD 178 Query: 178 VDIQRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVAL 237 +D++ LV+ AR+ LR F A MGI+G NFAVA+TGT+ +VTNEGN R+ TT+P VHVAL Sbjct: 179 LDVEGLVRFARKVLRHKFLEAGMGITGGNFAVADTGTVAIVTNEGNGRMCTTVPPVHVAL 238 Query: 238 AGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNG 297 G++KL+P++ D L +L +ATGQ +SY++ G +G +E H+V LDNG Sbjct: 239 VGIEKLIPSIKDLPDFLSLLTCSATGQRASSYISMTTGPRRTNE-TEGPEEFHVVLLDNG 297 Query: 298 RRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKAR 357 R ++A P + ++L C+ CG+C N CPVY VGGH Y G +G +L+ G+ Sbjct: 298 RSSIAASP-WREMLHCLHCGSCLNHCPVYHAVGGHAYESSYPGPMGSVLSTLLWGKQSYP 356 Query: 358 NLVQNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKN-----RKL 412 L C C C +CA I L + +R + G +T+ + L + R+ Sbjct: 357 ELANACTLCGRCVDVCAVKIPLANYHRTLR----HQGGSNSQTSYLAARLASHPGAYRRG 412 Query: 413 FHTLLRFAKWAQKPVTGGTPYIRHLPQIFAKDHGFKALP-AIADKPFRDEWETVRPRIAK 471 H L R + +P+T P I + A + LP A ++PFRD W +P+ Sbjct: 413 IHALRRMLR--TQPLTKVLPKIN---KSVANWQSCRVLPVAGEEQPFRDWWHQHQPKGQA 467 Query: 472 PKLR 475 PKL+ Sbjct: 468 PKLK 471 Score = 36.6 bits (83), Expect = 4e-06 Identities = 18/53 (33%), Positives = 31/53 (58%) Query: 196 ATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLH 248 A A +GI+ ++ +AETG++ GN L + LP VH+A++ L+ L+ Sbjct: 575 ANAQLGITYSSAFLAETGSLIYPAGAGNGTLASLLPEVHLAISASSTLLSDLN 627 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: 1098 Number of extensions: 64 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 717 Length of database: 679 Length adjustment: 39 Effective length of query: 678 Effective length of database: 640 Effective search space: 433920 Effective search space used: 433920 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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