GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc7a1 in Chryseobacterium arthrosphaerae CC-VM-7

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_065398285.1 BBI00_RS08080 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>NCBI__GCF_001684965.1:WP_065398285.1
          Length = 560

 Score =  226 bits (575), Expect = 3e-63
 Identities = 145/440 (32%), Positives = 222/440 (50%), Gaps = 41/440 (9%)

Query: 12  QMLRRKVVDCSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAG-AVARENAGPAIVISF 70
           Q+ RRK+   +   + L R L  +D+V  G+ + +GAG +   G AV R   GP +++ +
Sbjct: 3   QLFRRKIYSDTDTSTGLLRVLGVWDIVFFGIAAIIGAGSFSSLGEAVFR--GGPGVILLY 60

Query: 71  LIAALASVLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVAR 130
           LI   A     LCY EF +R+P  GSAY Y+Y + GEL A+I GW LI+ Y  G   VA 
Sbjct: 61  LICGFACGFTALCYAEFASRIPTAGSAYTYAYASFGELIAWIIGWALIMEYSFGNIYVAF 120

Query: 131 AWSATFDELIG------------------KPIGEFSRQHMALNA------PGVLAQTPDI 166
           +WS  F   +G                  K +   S     LNA       G L    DI
Sbjct: 121 SWSDYFTSFLGRLGMHIPDYLTCSYTEARKAVQYGSENKELLNAWNTAPLIGSLKFIVDI 180

Query: 167 FAVIIIIILTGLLTLGVKESAMVNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSC 226
            A++I  ++T L  +GVKES   N     + + V+  +++ GF   +  NW         
Sbjct: 181 PALVINGLITWLCYVGVKESKNFNNSLVILKLGVIILVILVGFAYINTDNW--------- 231

Query: 227 NNNDTNVKYGEGGFMPFGFSGVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVAS 286
                +   G   FMP GF+GV+S  +  F+A++GFD ++   EE K+PQK +P G++ S
Sbjct: 232 --TPVSPATGMPSFMPNGFAGVMSAVSGVFFAYIGFDALSVLSEETKDPQKTLPKGMIIS 289

Query: 287 LLICFIAYFGVSAALTLMMPYFCLD-IDSPLPGAFKHQGWEEA--KYAVAIGSLCALSTS 343
           L++C + Y  ++  LT M+ Y   D +  PL   F+      A  +  V+  ++ A++T 
Sbjct: 290 LVLCTVIYIALTLVLTGMVDYKKFDGVGDPLSFIFEKTNANVAWMELIVSFVAIVAITTV 349

Query: 344 LLGSMFPMPRVIYAMAEDGLLFKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVD 403
           LL      PR+ YAM+ DGL+ +   KI+ + KTP  AT+ +G +  +     +   ++D
Sbjct: 350 LLVFQMGQPRIWYAMSRDGLMPQRFQKIHPKYKTPSYATIVTGIVVGIPILFTDKTFILD 409

Query: 404 LMSIGTLLAYSLVAACVLVL 423
             SIGT+ A+ LV A VLVL
Sbjct: 410 FTSIGTIFAFVLVCAGVLVL 429



 Score = 38.5 bits (88), Expect = 8e-07
 Identities = 15/45 (33%), Positives = 26/45 (57%)

Query: 558 VLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSE 602
           ++P++ +   +YL+  +    W  F +W LIG  IYF YG  +S+
Sbjct: 508 LIPLIGLSSCLYLLTGMSHENWFWFGMWFLIGMVIYFCYGYKNSK 552


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: 936
Number of extensions: 50
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 560
Length adjustment: 37
Effective length of query: 585
Effective length of database: 523
Effective search space:   305955
Effective search space used:   305955
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.

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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