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_036136365.1 N800_RS06840 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>NCBI__GCF_000768355.1:WP_036136365.1
          Length = 474

 Score =  247 bits (630), Expect = 9e-70
 Identities = 144/417 (34%), Positives = 231/417 (55%), Gaps = 36/417 (8%)

Query: 28  LSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCYGEF 87
           L R L  + L ALG+G+ +G G++V+ G  A ++AGPAI++SF++AA+      L Y EF
Sbjct: 23  LHRTLGKWGLTALGIGAVIGGGIFVITGQAAADHAGPAIMLSFVLAAICCTFCALAYAEF 82

Query: 88  GARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKPIGEF 147
            + VP +GSAY Y+Y T+GEL A+  GW L+L Y +  S+VA +W+  F  L+       
Sbjct: 83  ASMVPVSGSAYTYTYATLGELAAWFIGWMLVLEYGVSASAVAVSWTGYFLSLL------- 135

Query: 148 SRQHMALNAPGVLAQTP------------DIFAVIIIIILTGLLTLGVKESAMVNKIFTC 195
             +H  ++ P  L Q P            ++ A  I+++LT +  +G+++S+ +N     
Sbjct: 136 --EHFNIHLPAALVQAPLDSKLQPTGAIANLPAAAIVLLLTWVCYIGIRKSSGMNTAMVL 193

Query: 196 INVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATC 255
           +   ++  ++++G+      NW   E     N        G G    FG+ GVL GA+  
Sbjct: 194 LKSGLIVLVIIAGWQYVDPANW---EPFIPANE-------GPG---KFGWEGVLRGASMV 240

Query: 256 FYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLDIDSP 315
           F+A++GF+ ++   +E  NPQK +P G++ SL IC + Y G++A +T + PY  L  D P
Sbjct: 241 FFAYIGFEAVSVAAQESHNPQKDLPFGMLMSLAICTVLYIGMAAVMTGLTPYTLLGTDEP 300

Query: 316 LPGAFK-HQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNR 374
           +  A   H      +  V IG+L  LS+ +L  +   PR+   MA DGLL +   +I+ +
Sbjct: 301 VVTAVAGHAELAWLRVVVEIGALIGLSSVVLVMIIGQPRIFMIMARDGLLPEVFTRIHPK 360

Query: 375 TKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVL-RYQPEQP 430
            +TP I TV +G   A++A +F L  L +L S+GTL+A+  V A VL+L R QP+ P
Sbjct: 361 HRTPHINTVITGIGIALLAAVFPLDILGELTSMGTLIAFGAVCAGVLILRRTQPDLP 417



 Score = 42.7 bits (99), Expect = 4e-08
 Identities = 57/226 (25%), Positives = 88/226 (38%), Gaps = 44/226 (19%)

Query: 377 TPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRYQPEQPNLVYQM 436
           TP     T   +   +A   EL  L  ++ IG L+  S V   +++      QP +   M
Sbjct: 290 TPYTLLGTDEPVVTAVAGHAELAWLRVVVEIGALIGLSSVVLVMII-----GQPRIFMIM 344

Query: 437 ARTTEELDRVDQNELVSASESQTGFLPVAEKFSLKSILSPKNVEPSKFSGLIVNISAGLL 496
           AR                     G LP  E F+    + PK+  P      I  +  G+ 
Sbjct: 345 ARD--------------------GLLP--EVFTR---IHPKHRTPH-----INTVITGIG 374

Query: 497 AALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLSFKVPFV 556
            AL+  V  + +LG E  + GTL A   +   VL        I R+ +      F++  V
Sbjct: 375 IALLAAVFPLDILG-ELTSMGTLIAFGAVCAGVL--------ILRRTQPDLPRPFRIRGV 425

Query: 557 PVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSE 602
             + +  IF  + L+  +    W+    W  +GF IYF YG  HS+
Sbjct: 426 WFVCLAGIFSCLALLSAMTLHNWMLMLGWTTVGFAIYFLYGYRHSK 471


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: 735
Number of extensions: 29
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: 474
Length adjustment: 35
Effective length of query: 587
Effective length of database: 439
Effective search space:   257693
Effective search space used:   257693
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: 52 (24.6 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