Align Citrate/succinate antiporter; Citrate carrier; Citrate transporter (characterized)
to candidate HSERO_RS04820 HSERO_RS04820 C4-dicarboxylate ABC transporter
Query= SwissProt::P0AE74 (487 letters) >FitnessBrowser__HerbieS:HSERO_RS04820 Length = 501 Score = 286 bits (731), Expect = 1e-81 Identities = 162/496 (32%), Positives = 263/496 (53%), Gaps = 30/496 (6%) Query: 9 WKLLAPLVVMGVMF---LIPVPDGMPPQAWHYFAVFVAMIVGMILEPIPATAISFIAVTI 65 +KL+ L+ V+ L P P G+ P+AW A+F+ IV +IL+ +P ++ +A+ I Sbjct: 18 FKLVPALIATAVLIALLLTPCPTGLEPKAWALVAIFLTTIVAIILKVMPIGVMAMMAIVI 77 Query: 66 CVIGSNYLLFDAKELADPAFNAQKQALKWGLAGFSSTTVWLVFGAFIFALGYEVSGLGRR 125 L+ + K A+ LA FS+ +WL+ A + + G + +GLGRR Sbjct: 78 V------------SLSQVTSTSSKGAITDALASFSNPLIWLIVVAILISRGLKKTGLGRR 125 Query: 126 IALFLVKFMGKRTLTLGYAIVIIDILLAPFTPSNTARTGGTVFPVIKNLPPLFKSFPNDP 185 + L + +GKRT+ +GY + I +++LAPFTPSNTAR GG V P++K++ F S P Sbjct: 126 VGLMFIALLGKRTIGIGYGLAICELVLAPFTPSNTARGGGIVHPIMKSIANAFDSDPAKG 185 Query: 186 SARRIGGYLMWMMVISTSLSSSMFVTGAAPNVLGLEFVSKIAG--IQISWLQWFLCFLPV 243 + ++G YL + + ++S+MF+T APN L + +V+K G +Q++W W LC L Sbjct: 186 TQNKVGSYLALVNYHANPITSAMFLTATAPNPLVVNYVAKATGHALQLTWTTWALCMLLP 245 Query: 244 GVILLIIAPWLSYVLYKPEITHSEEVATWAGDELKTMGALTRREWTLIGLVLLSLGLW-- 301 G++ L+I P + Y+L PE+ + +A EL MG L E ++G L L LW Sbjct: 246 GLVCLLIMPMVIYLLSPPELKSTPNAVDYARSELDKMGKLGASEKVMLGTFALLLLLWAN 305 Query: 302 -----VFGSEVINATAVGLLAVSLMLALHVVPWKDITRYNSAWNTLVNLATLVVMANGLT 356 + + ++ T V + + +++ + W D+ SAW+TLV LV++A L Sbjct: 306 VPAMLLGAAFTLDPTVVAFVGLFVLIITGTIDWDDVLSEKSAWDTLVWFGALVMLAEQLN 365 Query: 357 RSGFIDWFAGTMSTHL--EGFSPNATVIVLVLVFYFAHYLFASLSAHTATMLPVILAVG- 413 ++G + WF+ M + G A VL+LVF +HY FAS +AH + M+ L VG Sbjct: 366 KTGVVAWFSEGMKAAIVASGMGWIAVAAVLLLVFVLSHYFFASTTAHISAMMLAFLTVGA 425 Query: 414 KGIPGVPMEQLCILLVLSIGIMGCLTPYATGPGVIIYGCGYVKSKDYWRLGAIFGVIYIS 473 + +P + +++ G+M LT YATG II+G GYV +W +G + V+ + Sbjct: 426 QLLPPQYVVPFMLMMTAGSGVMMTLTHYATGTSPIIFGSGYVSMGKWWGVGFVMAVVELL 485 Query: 474 MLLLVG---WPILAMW 486 + VG W L W Sbjct: 486 VFATVGMVWWKGLGYW 501 Lambda K H 0.328 0.142 0.453 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: 769 Number of extensions: 48 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: 487 Length of database: 501 Length adjustment: 34 Effective length of query: 453 Effective length of database: 467 Effective search space: 211551 Effective search space used: 211551 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 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