GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Mesorhizobium ciceri WSM1271

Align TRAP C4-dicarboxylate transport system permease, DctM-2 subunit, component of The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, KD=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, KD=3 μM]) (characterized)
to candidate YP_004139565.1 Mesci_0342 TRAP dicarboxylate transporter subunit DctM

Query= TCDB::D5ATK1
         (611 letters)



>NCBI__GCF_000185905.1:YP_004139565.1
          Length = 593

 Score =  826 bits (2133), Expect = 0.0
 Identities = 437/604 (72%), Positives = 491/604 (81%), Gaps = 23/604 (3%)

Query: 3   MELIAQNMAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELAPLSGGSINLDWPLLN 62
           ME IAQNMAPIMF SLI+FLL+GYPVAFSLAANGL+FF IGV L+P SGGSINL WPLL+
Sbjct: 1   MEFIAQNMAPIMFASLIIFLLIGYPVAFSLAANGLMFFFIGVLLSPYSGGSINLAWPLLH 60

Query: 63  AMPERFWG--VLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVIL 120
           A+P+ F+G  V+SN+TLLAIPFFTFMGI+LE+SGMAEDLLDTIGQLFGPIRGGLAYAVI 
Sbjct: 61  ALPDNFYGSRVMSNDTLLAIPFFTFMGIVLERSGMAEDLLDTIGQLFGPIRGGLAYAVIF 120

Query: 121 VGALLAATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVL 180
           VGALLAATTGVVAASVIAMGLISLPIMLRYGYDRR+ASGVIAASGTLAQIIPPSLVLIVL
Sbjct: 121 VGALLAATTGVVAASVIAMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIVL 180

Query: 181 ADQLGRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTLGQGVLSFFV 240
           ADQLGRSVGDMY GALIPGLVLTGLYM Y+L+MSI+RPNSMPALP EARTLG GV+S  V
Sbjct: 181 ADQLGRSVGDMYAGALIPGLVLTGLYMSYILIMSIIRPNSMPALPLEARTLGHGVMSLLV 240

Query: 241 AMGIGIAIFVAAQHWLAGTGAAKNAGILAASIAVIFVYVMALIDKATGLDRMSHLAQQVI 300
           A+ +  A+  AA  +LA      NA IL A+  V+F+Y++A+ DK    + MS LAQQVI
Sbjct: 241 ALLVTSAVSYAAYRYLA-PAHGDNADILGATAGVLFIYIVAIADKRLNFNMMSRLAQQVI 299

Query: 301 IVLIPPLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKKRLSLEVVREALAATTRL 360
           IVLIPPLALIFLVLGTIFLGIATPTEGGAMG+VGAL ++A K RLSL+VV++ALA+TTRL
Sbjct: 300 IVLIPPLALIFLVLGTIFLGIATPTEGGAMGSVGALFMAAAKGRLSLDVVKQALASTTRL 359

Query: 361 SAFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLIFVSLLVFFLAFFLDFFE 420
           S+FV+FIL+GARVFSLTFYGVNGHIWVEHLL SLPGGE GFLI V++LVFFLAFFLDFFE
Sbjct: 360 SSFVLFILIGARVFSLTFYGVNGHIWVEHLLTSLPGGEVGFLIGVNMLVFFLAFFLDFFE 419

Query: 421 LAFIIVPLLVAPAEALGIDLIWFGVILGVNMQTSFMHPPFGFALFFLRSVAPKVPFLDKV 480
           LAFIIVPLL   A+ LGIDLIWFGV+LGVNMQTSFMHPPFGFALF+LRSVA +VP+LD++
Sbjct: 420 LAFIIVPLLAPAADKLGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAARVPYLDRL 479

Query: 481 TGKLTEPVKTSQIYWGAVPFVCIQIVMIAVVIAFPQLVMHYKGKPVDVSHVTVTVPGGIG 540
           TGK   PV T QIYWGAVPFVCIQ++MI + IAFPQ+VMHYKG  VD   +   VP    
Sbjct: 480 TGKQIAPVTTGQIYWGAVPFVCIQVIMIGLTIAFPQMVMHYKGTTVDPGTIDYKVP---- 535

Query: 541 GGLGGGLGMPGGLGLPPIGAQP--GAVPAPGGLGGLPPGLGAPAG----QPVTPPAGGAS 594
                   +P   GL P+G  P  GA PA G      P L  P       P  P A    
Sbjct: 536 -------EVP---GLSPLGTPPADGAAPAGGATAPAAPDLSQPPSFGDPTPAKPAAPQPD 585

Query: 595 LGIP 598
           L  P
Sbjct: 586 LSQP 589


Lambda     K      H
   0.327    0.146    0.437 

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: 1090
Number of extensions: 49
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: 611
Length of database: 593
Length adjustment: 37
Effective length of query: 574
Effective length of database: 556
Effective search space:   319144
Effective search space used:   319144
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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