Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate WP_011386479.1 AMB_RS20890 iron-sulfur cluster-binding protein
Query= uniprot:Q726S3 (717 letters) >NCBI__GCF_000009985.1:WP_011386479.1 Length = 478 Score = 272 bits (696), Expect = 2e-77 Identities = 175/452 (38%), Positives = 234/452 (51%), Gaps = 21/452 (4%) Query: 24 RNAMDKFAVAYRASRANAFKDIDE-KAIIAEVADAKDHAAKNMDTLYAQFKAEAEKRGVK 82 R AMD RA F D E A+ A A A+ +A + L Q +A + G+ Sbjct: 28 RRAMD----GLMTKRAAQFADEAEWNALRARGAAARANALAKLPELLEQLEANCLRNGIH 83 Query: 83 VHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWII 142 VH A T AEAN I+ I + IK KSM EE HLN LE+ + +E+DLGE+II Sbjct: 84 VHWAETTAEANAIVLGILEAAGARTVIKGKSMVTEEMHLNAHLEKHGITPVESDLGEYII 143 Query: 143 QMRHEGPSHMVMPAIHLSRYQVADLFSE-VTKQKQEVDIQRLVKVARRELRTHFATADMG 201 Q+ E PSH+VMP IH ++ ++A+LF + + Q ++ L AR LR FA AD G Sbjct: 144 QLAGEAPSHIVMPCIHKNKTEIAELFHDKIEGQPYTENVDELTAAARAALRGAFAGADAG 203 Query: 202 ISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNA 261 ISG NFAVAETGT+ L+ NEGN RL TTLP +H+A+ G++K++ L D L +LPR+A Sbjct: 204 ISGVNFAVAETGTLVLIENEGNGRLSTTLPPLHIAVTGIEKVLEKLDDVPPLLSLLPRSA 263 Query: 262 TGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPLFSQVLRCVRCGACAN 321 TGQ IT+YV I + E DG K +H+V LDNGR + D LRC+RC AC N Sbjct: 264 TGQPITTYVNMISSPRK-EGEKDGPKAVHLVLLDNGRSRVHGDTELRDTLRCIRCAACMN 322 Query: 322 VCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCESCKHICAGGIDLPR 381 CPVY VGGH Y G IG +LT G D A + C +C +C I +P Sbjct: 323 HCPVYTRVGGHTYTFTYPGPIGKLLTPQIEGLDCAGDQPHASTLCRACADVCPVQIPIPD 382 Query: 382 LIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFAKWAQKPVTGGTPYIRHLPQIF 441 L+ RL E P + G+ +K T W + +P + +I Sbjct: 383 LL----VRLRTESVRPTQ----GQAVKGAGSSATTSETLGWKGWTLLYASPLVY---RIG 431 Query: 442 AKDHGFKALPAIADKPFRDEWETVRPRIAKPK 473 K G+ + P +W +VR KPK Sbjct: 432 TKMLGWFGNLMPSSAPMLKQWTSVR---TKPK 460 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: 767 Number of extensions: 42 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: 717 Length of database: 478 Length adjustment: 37 Effective length of query: 680 Effective length of database: 441 Effective search space: 299880 Effective search space used: 299880 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