Alignments for a candidate for Slc7a1 in Streptococcus oralis 7747

GapMind for catabolism of small carbon sources

Alignments for a candidate for Slc7a1 in Streptococcus oralis 7747

Align Cationic amino acid transporter 3 (characterized)
to candidate WP_038806034.1 HK29_RS04105 amino acid permease

Query= CharProtDB::CH_091036
         (618 letters)



>NCBI__GCF_000382825.1:WP_038806034.1
          Length = 465

 Score =  198 bits (503), Expect = 5e-55
 Identities = 141/485 (29%), Positives = 251/485 (51%), Gaps = 39/485 (8%)

Query: 17  RVLELGMGETRLARCLSTLDLVALGVGSTLGAGVYVLAGEVAKDKAGPSIVICFLVAALS 76
           R  ++ +G T + R L   DL+ LG+G+ +G G++ + G  A   AGPS+V+  +++AL 
Sbjct: 5   RTKDVSLGRTEMHRHLKLWDLILLGIGAMVGTGIFTITGTAAATLAGPSLVVSIVISALC 64

Query: 77  SVLAGLCYAEFGARVPGSGSAYLYSYVTVGELWAFTTGWNLILSYVIGTASVARAWSSAF 136
             L+ L +AEF +RVP +G AY Y Y  +GEL A+  GW  I+ ++   + VA  W++ F
Sbjct: 65  VSLSALFFAEFASRVPATGGAYSYLYAILGELPAWIAGWLTIMEFMTAVSGVASGWAAYF 124

Query: 137 DNLIGNH---ISRTLKGTILLKMPHVLAEYPDFFALALVLLLTGLLVLGASKSALVTKVF 193
             L+ N+   + + L GT   +       Y D   + ++ L+TGL++L  SK+AL    F
Sbjct: 125 KGLLSNYGISMPQALNGTFNPEQD----TYIDLLPILVLALVTGLVLLN-SKAAL---RF 176

Query: 194 TGMNLLVLSFVIISGFIKGELRNWKLTKEDYCLTMSESNGTCSLDSMGSGGFMPFGLEGI 253
             + L+VL F  ++ FI   +  W +  E++           +L   G G     G  G+
Sbjct: 177 NSL-LVVLKFSALALFILVGI--WYIKPENW----------SNLAPFGFGQLYG-GSTGV 222

Query: 254 LRGAATCFYAFVGFDCIATTGEEAQNPQRSIPMGIVISMFICFLAYFGVSSALTLMMPYY 313
           + GA+  F+ F+GF+ I+   +E Q+PQ++IP GIV+S+ I  + Y  V+  LT ++ Y 
Sbjct: 223 MAGASLMFFGFLGFESISMAVDEIQSPQKNIPRGIVLSLTIVTILYALVTIVLTGIVHYS 282

Query: 314 KLHPESPLPEAFSYVGWEPARYLVAIGSLCALSTSLLGSMFPMPRVMYSMAEDGLLFRVL 373
           +L+ +  +  +   +G   A   V++ ++  L T  +   + + R++YS+A DGLL +  
Sbjct: 283 QLNVDDAVAFSLRSIGIGWAANYVSLVAILTLITVCISMTYALSRMIYSLARDGLLPQSF 342

Query: 374 AKVHSVTHIPIVATLVSGVIAAFMAFLFELTDLVDLMSIGTLLAHSLVSICVLILRYQPD 433
            ++   + +P  AT+++GV +A  A +F L  +   ++I TL    L+ +   I++ + D
Sbjct: 343 KQLSKTSRVPKNATILTGVASAIAAGVFPLASIAAFLNICTLA--YLILLAYGIIKLRKD 400

Query: 434 QEMKSVEEEMELQEETLEAEKLTVQALFCPVNSIPTLLSGRVVYVCSSLLAVLLTVLCLV 493
           + M              E E  T      P+ SI   LS  + Y   + +A  L +L  +
Sbjct: 401 KGMPK------------EGEFKTPLVPLLPILSILICLSFMLQYTKETWIAFGLALLVGL 448

Query: 494 LTWWT 498
           + ++T
Sbjct: 449 VIYFT 453



 Score = 62.8 bits (151), Expect = 3e-14
 Identities = 32/73 (43%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 518 LILAISGVIWRQPQNRTPLH--FKVPAVPLLPLVSIFVNVYLMMQMTAGTWARFGIWMLI 575
           LIL   G+I  +     P    FK P VPLLP++SI + +  M+Q T  TW  FG+ +L+
Sbjct: 387 LILLAYGIIKLRKDKGMPKEGEFKTPLVPLLPILSILICLSFMLQYTKETWIAFGLALLV 446

Query: 576 GFAIYFGYGIQHS 588
           G  IYF YG +HS
Sbjct: 447 GLVIYFTYGYRHS 459


Lambda     K      H
   0.326    0.139    0.425 

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: 695
Number of extensions: 39
Number of successful extensions: 3
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: 618
Length of database: 465
Length adjustment: 35
Effective length of query: 583
Effective length of database: 430
Effective search space:   250690
Effective search space used:   250690
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: 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources