Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_086510923.1 BZY95_RS16160 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_002151265.1:WP_086510923.1 Length = 427 Score = 365 bits (937), Expect = e-105 Identities = 186/426 (43%), Positives = 274/426 (64%), Gaps = 2/426 (0%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPF 60 ME +L G F++L+++G+P+A+ALG+S+L I L + ++ SG++ F LL IP Sbjct: 1 MEVMVLFGVFLLLLVLGLPIAFALGISSLAYLLLEGISLTIVPQRMYSGIDTFVLLCIPG 60 Query: 61 FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV 120 FVLAG +M G ++ +V F+ +VG +RGGL L N+ S FG ISG++VAD AS+GSV Sbjct: 61 FVLAGNLMNVGNITEHIVRFSNAVVGHIRGGLGLANVGGSMIFGGISGTAVADAASIGSV 120 Query: 121 LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGL 180 +IP M R GY + F+ AVT + S + PPS ++ AG VS+ +F+AG +PGL Sbjct: 121 MIPGMARSGYDKPFAAAVTAASSTIGPIIPPSVPMIIVGSLAG--VSVGRMFLAGAVPGL 178 Query: 181 LLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATE 240 LL MM + A KR YPKG LRE L+ A W L+ VIIL GI+ G FT TE Sbjct: 179 LLGVAMMITVYLLAVKRGYPKGRRATLRELLREGRTAFWALLMTVIILYGIIGGFFTPTE 238 Query: 241 SAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPS 300 ++ VA +++ V M++Y+ WR LP ++ TV T S +++L+G A FG+++T QIP Sbjct: 239 ASIVASLYALVVGMYVYKGLTWRKLPAILTDTVLTSSALLLLVGLANLFGWILTSQQIPQ 298 Query: 301 KITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGM 360 I + +SDN V+++ +N +L+ +G M+ ++IL P LL V TGIG+DPVHF + Sbjct: 299 TIAALIMAISDNPIVVILILNLILLFVGAFMETIAALIILFPALLGVATGIGMDPVHFAV 358 Query: 361 IMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLW 420 + ++NL IGL TPPVG LFV S IGK+ + + +A++PF + LVL+ V Y+PAISLW Sbjct: 359 MAVLNLMIGLTTPPVGVCLFVVSGIGKLQMLTVARAILPFLVCNILVLLLVAYVPAISLW 418 Query: 421 LPSVVL 426 LP +++ Sbjct: 419 LPDLLM 424 Lambda K H 0.329 0.142 0.418 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: 588 Number of extensions: 27 Number of successful extensions: 3 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: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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