Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate WP_011386479.1 AMB_RS20890 iron-sulfur cluster-binding protein
Query= uniprot:E4PLR6 (483 letters) >NCBI__GCF_000009985.1:WP_011386479.1 Length = 478 Score = 518 bits (1334), Expect = e-151 Identities = 265/463 (57%), Positives = 326/463 (70%), Gaps = 5/463 (1%) Query: 13 DFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALSRLPD 72 +F +A AL D +LR NFR AMD LMTKRA F D E LR G +A AL++LP+ Sbjct: 9 EFGAKAHVALNDPKLRANFRRAMDGLMTKRAAQFADEAEWNALRARGAAARANALAKLPE 68 Query: 73 LLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAE 132 LLEQLE NG+ VHWAET EAN++V GI+EA V+KGKSMV+EEM +N +L + Sbjct: 69 LLEQLEANCLRNGIHVHWAETTAEANAIVLGILEAAGARTVIKGKSMVTEEMHLNAHLEK 128 Query: 133 RGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKL-GEPETEDVNQLIQI 191 G+ +ESD+GEYI+QL E PSHI+MP IHKN ++++LFHDK+ G+P TE+V++L Sbjct: 129 HGITPVESDLGEYIIQLAGEAPSHIVMPCIHKNKTEIAELFHDKIEGQPYTENVDELTAA 188 Query: 192 GRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPN 251 R LR F AD G+SGVNFA+AETGTL+L+ENEGNGR+STT PP+HIAVTGIEKV+ Sbjct: 189 ARAALRGAFAGADAGISGVNFAVAETGTLVLIENEGNGRLSTTLPPLHIAVTGIEKVLEK 248 Query: 252 LRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFADAQM 311 L DV PL+SLL RSA GQPITTYVN+IS PRK E DGP+ VHLVLLDNGR+ D ++ Sbjct: 249 LDDVPPLLSLLPRSATGQPITTYVNMISSPRKEGEKDGPKAVHLVLLDNGRSRVHGDTEL 308 Query: 312 RQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLCG 371 R TL CIRC ACMNHCPVYTRVGGHTY YPGPIGK++TP + GLD D P AS+LC Sbjct: 309 RDTLRCIRCAACMNHCPVYTRVGGHTYTFTYPGPIGKLLTPQIEGLDCAGDQPHASTLCR 368 Query: 372 ACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRGWQMLNTRPAL 431 AC +VCPV+IPIP+LL RLR E+V+ P Q Q VKG G+ + +E W+GW +L P + Sbjct: 369 ACADVCPVQIPIPDLLVRLRTESVR-PTQGQAVKGAGSSATTSETLGWKGWTLLYASPLV 427 Query: 432 YRSFLWAATRFRALAPKKA---GPWTENHSAPVPARRSLHDLA 471 YR F L P A WT + P A +SLH+LA Sbjct: 428 YRIGTKMLGWFGNLMPSSAPMLKQWTSVRTKPKFAPKSLHELA 470 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: 620 Number of extensions: 24 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: 483 Length of database: 478 Length adjustment: 34 Effective length of query: 449 Effective length of database: 444 Effective search space: 199356 Effective search space used: 199356 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 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