Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate PP_2185 PP_2185 putative Formate dehydrogenase, alpha subunit
Query= uniprot:Q39TW6 (218 letters) >FitnessBrowser__Putida:PP_2185 Length = 960 Score = 104 bits (259), Expect = 7e-27 Identities = 71/240 (29%), Positives = 111/240 (46%), Gaps = 40/240 (16%) Query: 3 EINLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVE-VRGWPK 61 +++L IDG+ + G +++ AA +G SIP LC + LE +G CR+C VE+E +RG+P Sbjct: 25 QVSLSIDGRAISVPAGTSVMRAAAMLGTSIPKLCATDSLEAFGSCRMCMVEIEGMRGYP- 83 Query: 62 LVAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAP---------DSEELKALAQEYG 112 A C PV +G+VVRT ++ +R+ ++E ++ P + EL+ +A + G Sbjct: 84 --ASCTTPVSEGMVVRTETPRLAGLRRNVMELYISDHPLDCLTCSANGNCELQTVAGQVG 141 Query: 113 ADRDR-------------------FEKHPSFCIHCGLCVRYCAEIKKKNAVGFVDRGSNR 153 R F+ PS CI C CVR C +I+ A+ RG Sbjct: 142 LREVRYGYDGANHLDEKKDVSNPYFDYEPSKCIVCSRCVRACEDIQGTFALTITGRGFES 201 Query: 154 EISFI--PEIAAKECWDCKECFPLCPTSALQAAYVLAGALMTPPEEA---HSGGCGCSCS 208 ++ A EC C C CPT+ L ++ + PE + CG CS Sbjct: 202 RVAAAGGENFLASECVSCGACVQTCPTATLTEKSLVQ---LGQPERSVITTCAYCGVGCS 258 Lambda K H 0.320 0.137 0.432 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: 476 Number of extensions: 21 Number of successful extensions: 6 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: 218 Length of database: 960 Length adjustment: 33 Effective length of query: 185 Effective length of database: 927 Effective search space: 171495 Effective search space used: 171495 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 (21.8 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