GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT1 in Methylocystis bryophila S285

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>NCBI__GCF_002117405.1:WP_085770386.1
          Length = 488

 Score =  225 bits (573), Expect = 4e-63
 Identities = 132/409 (32%), Positives = 216/409 (52%), Gaps = 24/409 (5%)

Query: 24  EESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLC 83
           E   L R L  + LV +G+G  +G G++VL G VA   AGP + +SFLIA +AS  A LC
Sbjct: 21  ERGALRRALGLWQLVGIGLGGLIGVGIFVLTGVVAATQAGPGVALSFLIAGVASGAAALC 80

Query: 84  YGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKP 143
           Y EF + +P  GSAY Y+Y  +GEL A+I GW+L+L Y +  + V+  WS     L+   
Sbjct: 81  YAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLEYALVVAVVSIGWSGYLRALLA-- 138

Query: 144 IGEFSRQHMALNAPGVL-AQTPDIFAVIIIIILTGLLTLGVKESAMVNKIFTCINVLVLC 202
           +   +    A  APG       D+FA++    +  LLTL V+  A  N     + +  + 
Sbjct: 139 LFGVAPPEWAAGAPGTGDGHILDLFAMLGAFGVALLLTLRVEWGARFNTAMVLLKIAAVI 198

Query: 203 FIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCFYAFVGF 262
            ++++     +  NW+                     FMPFGF GV+ GAA  F+A  G+
Sbjct: 199 VVILAAAPHINPANWR--------------------PFMPFGFGGVVEGAAVVFFAVFGY 238

Query: 263 DCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLDIDSPLPGAFKH 322
           D + T GEE   PQ+ +P  ++ SL++    Y  +S ALT +  Y  LD  +P+  AF  
Sbjct: 239 DTLTTAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLALTGIARYDTLDNAAPVASAFAA 298

Query: 323 QGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNRTKTPVIAT 382
            G   A   V+  ++  + + +L  +    R+ +AM+ DGLL  + A+ + +  TP   T
Sbjct: 299 LGMGWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSRDGLLPAWFARPHPQFATPYRPT 358

Query: 383 VTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRY-QPEQP 430
           + +G + A+++  F ++++ +L++IGTL A+ ++   V+ LR+ +P+ P
Sbjct: 359 LIAGGLCALVSAFFPIREVAELVNIGTLSAFVVICLAVIALRHTRPDVP 407



 Score = 55.8 bits (133), Expect = 4e-12
 Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 2/80 (2%)

Query: 525 MTGSVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAV 584
           ++  V++C+ V  +   +P+      F+ P  P LP++ +  +++L+ +L    W RF V
Sbjct: 386 LSAFVVICLAVIALRHTRPD--VPRGFRAPLSPYLPLIGVGFSLWLLSKLPAIAWERFVV 443

Query: 585 WMLIGFTIYFGYGIWHSEEA 604
           W++IG  +YF YG  HS  A
Sbjct: 444 WLIIGLAVYFLYGRRHSRLA 463


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: 759
Number of extensions: 26
Number of successful extensions: 4
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: 488
Length adjustment: 36
Effective length of query: 586
Effective length of database: 452
Effective search space:   264872
Effective search space used:   264872
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 Apr 09 2024. 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