Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate WP_057508034.1 ABB28_RS07345 citrate transporter
Query= TCDB::P42308 (426 letters) >NCBI__GCF_001431535.1:WP_057508034.1 Length = 442 Score = 541 bits (1393), Expect = e-158 Identities = 266/437 (60%), Positives = 341/437 (78%), Gaps = 14/437 (3%) Query: 1 MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60 ML+ILGF M+I FMYLIMS RLS L+ALI VPI+FAL+ GFG + EMM+ G+ +APTG Sbjct: 1 MLSILGFGMVITFMYLIMSKRLSPLVALITVPIIFALLGGFGAGIDEMMLDGIKKIAPTG 60 Query: 61 IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120 +ML+FAILYFG+MID+GLFDPL+ IL+ VKGDPLKI +GTAVL M ISLDGDG+TTYMI Sbjct: 61 VMLMFAILYFGVMIDAGLFDPLVRVILNVVKGDPLKIVMGTAVLAMLISLDGDGSTTYMI 120 Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMNIIPWGGPTARVLASLKLDTSEVFTPLIPA 180 T++AMLPLY+RLGMN L + + +L GVMN+ PWGGPTAR +L +D ++VF PLIP+ Sbjct: 121 TVSAMLPLYRRLGMNALNMTCVTILAGGVMNLTPWGGPTARAATALHVDPADVFVPLIPS 180 Query: 181 MIAGILWVIAVAYILGKKERKRLGVISI-------DHAPSSDPEAAP-------LKRPAL 226 M+ ++ +A+ LG KER+RLGV+++ D + S D +A P +KRP L Sbjct: 181 MVIACAGILVLAWYLGMKERRRLGVMTLPQGGSWMDSSVSDDGDALPTVEDAEDIKRPKL 240 Query: 227 QWFNLLLTVALMAALITSLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVS 286 W N LT ALMAALI LLP+P+LFM FA+AL++NYPN+ EQ++R+ HAGN L+VVS Sbjct: 241 LWVNFGLTAALMAALIMGLLPMPILFMVGFAIALVINYPNLAEQRRRVVNHAGNVLSVVS 300 Query: 287 MVFAAGIFTGILSGTKMVDAMAHSLVSLIPDAMGPHLPLITAIVSMPFTFFMSNDAFYFG 346 ++FAAGIFTGIL+ T MV+AM+HS +++IP++ GP+L +ITA+ SMPFTFFMSNDAFYFG Sbjct: 301 LIFAAGIFTGILNNTGMVEAMSHSFLAIIPESWGPYLAVITALASMPFTFFMSNDAFYFG 360 Query: 347 VLPIIAEAASAYGIDAAEIGRASLLGQPVHLLSPLVPSTYLLVGMAGVSFGDHQKFTIKW 406 VLPI++EAA YGI E+ RASL GQPVHLLSPLVPSTYLLVG+A V F DHQKFT+KW Sbjct: 361 VLPILSEAAGNYGITPVEMARASLAGQPVHLLSPLVPSTYLLVGLAKVEFADHQKFTLKW 420 Query: 407 AVGTTIVMTIAALLIGI 423 AV ++++ +LL + Sbjct: 421 AVLISLLLMAGSLLFAL 437 Lambda K H 0.328 0.142 0.411 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: 793 Number of extensions: 39 Number of successful extensions: 2 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: 426 Length of database: 442 Length adjustment: 32 Effective length of query: 394 Effective length of database: 410 Effective search space: 161540 Effective search space used: 161540 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: 51 (24.3 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