GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc7a1 in Lysobacter daejeonensis GH1-9

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_036136362.1 N800_RS06835 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>NCBI__GCF_000768355.1:WP_036136362.1
          Length = 491

 Score =  281 bits (718), Expect = 6e-80
 Identities = 164/417 (39%), Positives = 239/417 (57%), Gaps = 36/417 (8%)

Query: 25  ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCY 84
           E  L R L    LV LGVG+ +GAG++V+ G  A   AGPA+++SF++AA+A   AGLCY
Sbjct: 30  EVTLKRVLTARHLVMLGVGAIIGAGIFVMTGTAAANYAGPAVILSFVMAAVACGFAGLCY 89

Query: 85  GEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELI---- 140
            EF + +P +GSAY Y+Y T+GE+ A+  GWNL+L Y+   SSVA  WS   +  +    
Sbjct: 90  AEFASMMPVSGSAYSYTYSTLGEVVAWFIGWNLVLEYLFAASSVAVGWSGYLNSFLTTHG 149

Query: 141 -GKPIG------EFSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAMVNKIF 193
            G P         +S +  +  + G +   P   AV+I+  ++GL   G+ +SA VN + 
Sbjct: 150 AGVPAALAQAPFHYSAETSSFVSTGSIVNLP---AVLIVAAISGLCYRGITQSAWVNALI 206

Query: 194 TCINVLVLCFIVVSGFVKGSIK--NWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSG 251
             I V V+  +   GF    I   NWQ              +   EGG   FG  GV+ G
Sbjct: 207 VAIKVTVI--VAFLGFAAQYINPDNWQ------------PFIPENEGG-TRFGTEGVVRG 251

Query: 252 AATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLD 311
           AA  F+A++GFD ++T   E KNPQ+ +P+GI+ SL +C + Y  V+A LT ++PY  LD
Sbjct: 252 AAVVFFAYIGFDAVSTAAGEAKNPQRDMPIGILGSLAVCTVLYIAVAATLTGLLPYPQLD 311

Query: 312 IDSPLP---GAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFL 368
              P+     A+   GW   K AV IG++  LS+ +L  +   PR+ YAMA+DGL+ K  
Sbjct: 312 TAKPVATALEAYPTLGW--LKMAVEIGAIAGLSSVILVMLMGQPRIFYAMAKDGLMPKIF 369

Query: 369 AKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRY 425
            +++ + +TP + TV  G +AA+MA L  L  L DL+S+GTLLA++ V A VL+LRY
Sbjct: 370 GRVHPKFQTPYVGTVIVGVVAAIMAGLLPLDFLGDLVSMGTLLAFATVCAGVLILRY 426



 Score = 47.0 bits (110), Expect = 2e-09
 Identities = 39/135 (28%), Positives = 61/135 (45%), Gaps = 12/135 (8%)

Query: 471 KSILSPK---NVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTG 527
           K  L PK    V P   +  +  +  G++AA++  +  +  LG + ++ GTL A   +  
Sbjct: 361 KDGLMPKIFGRVHPKFQTPYVGTVIVGVVAAIMAGLLPLDFLG-DLVSMGTLLAFATVCA 419

Query: 528 SVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWML 587
            VL        I R      +  F+VP   V+  L +   +YL  Q  +  W     W +
Sbjct: 420 GVL--------ILRYTRPDLQRPFRVPGAIVVCSLGVLSCLYLFWQPFKDHWQVMLGWTV 471

Query: 588 IGFTIYFGYGIWHSE 602
           IGF IYFGYG  +S+
Sbjct: 472 IGFVIYFGYGYRNSK 486


Lambda     K      H
   0.324    0.138    0.417 

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: 783
Number of extensions: 40
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 491
Length adjustment: 36
Effective length of query: 586
Effective length of database: 455
Effective search space:   266630
Effective search space used:   266630
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

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

Links

Downloads

Related tools

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