Alignments for a candidate for SSS-glucose in Alkalitalea saponilacus SC/BZ-SP2

GapMind for catabolism of small carbon sources

Alignments for a candidate for SSS-glucose in Alkalitalea saponilacus SC/BZ-SP2

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate WP_079555937.1 CDL62_RS06475 sodium/solute symporter

Query= SwissProt::P96169
         (543 letters)



>NCBI__GCF_002201795.1:WP_079555937.1
          Length = 631

 Score =  503 bits (1295), Expect = e-147
 Identities = 252/515 (48%), Positives = 365/515 (70%), Gaps = 23/515 (4%)

Query: 7   GLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANIS 66
           G + ID ++F  Y A+I+G+GLW+SR KKG +K ++DYFLAG +L WWA+GASLIAANIS
Sbjct: 4   GFTTIDYLIFGAYAALIMGIGLWISRTKKGEEKDSKDYFLAGGTLSWWAIGASLIAANIS 63

Query: 67  AEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKL 126
           AE FI MSGSGY+IGL +A+YEW++AI LI+V KY LP  ++K I+T+P+F  +R+   +
Sbjct: 64  AEHFIAMSGSGYAIGLGMAAYEWIAAIVLILVAKYLLPQMLDKKIFTMPQFARERYGSGV 123

Query: 127 KTILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVV 186
               + FW+ +Y+FVNLTSV +LG LA+  ILG+P++Y + GL +FA VYSIYGG+ +V 
Sbjct: 124 SFFFSFFWLLVYVFVNLTSVAWLGALAMNQILGVPILYGVPGLLIFAGVYSIYGGMKSVA 183

Query: 187 WTDVIQVFFLVLGGFMTTYMAVSFIGGTDG-----WFAGVSKMVDAA--PGHFEMILDQS 239
           WTD++QVFFL+ GG +T + A+  + G DG      F  V   + A+    HF MI+  S
Sbjct: 184 WTDIVQVFFLIFGGLITAWFALDAVAG-DGKSAFEGFRVVLNQIRASETDTHFNMIIGDS 242

Query: 240 ---NPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLI 296
                 ++NLPG+AV+ G +W+ N+ YWGFNQ+IIQ+ LAAK++ EA++G++FAA+LK++
Sbjct: 243 EGTRDSFLNLPGLAVIFGAMWLTNIGYWGFNQFIIQKGLAAKNLKEAKRGLLFAAYLKIL 302

Query: 297 VPFLVVLPGIAAYVI------TSDPQL--MASLGDIAATNLPSAANADKAYPWLTQ-FLP 347
           +P +V++PGI AYVI      T+D  L  +  +GD +       A +D AYPWL + F P
Sbjct: 303 IPIIVIIPGITAYVIHGMSVETADGSLAFINQMGD-STLLAGEVAISDDAYPWLLRNFAP 361

Query: 348 VGVKGVVFAALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVAL 407
           VG++G+ FAAL AA++SSLAS+LNST+TIFT+DIYK  I+  + + +LV VGR AA VAL
Sbjct: 362 VGIRGLAFAALVAAVISSLASLLNSTSTIFTLDIYKTLINKSASERQLVRVGRFAAFVAL 421

Query: 408 IIACLIA-PMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPF 466
            IA + A P+LGG+ QAFQYIQEYTG + PG++AVF +G+ WK+ T++ A+   +A+IP 
Sbjct: 422 AIAIVAARPLLGGLDQAFQYIQEYTGFIYPGVVAVFGMGILWKRATNRAALWTTIATIPT 481

Query: 467 ALFLKFMPLSMPFMDQMLYTLLFTMVVIAFTSLST 501
            + +K     +P+M +M Y  +  +V ++ T + T
Sbjct: 482 GILMKLALPDLPWMIRMGYVFII-LVGLSITLVLT 515



 Score = 39.7 bits (91), Expect = 3e-07
 Identities = 30/104 (28%), Positives = 47/104 (45%), Gaps = 12/104 (11%)

Query: 449 KKTTSKGAIIGVVASIPFA--------LFLKFMPLSMPFMDQMLYTLLFT-MVVIAFTSL 499
           KK  + G +   +A I F         LF   M L + F    + T + T + VI +T+ 
Sbjct: 531 KKQMNAGHVFAALAIITFVAGMLWGTNLFGMGM-LHLGFNSIFMTTAMMTFLAVIMYTNA 589

Query: 500 STSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLAVLYTLFW 543
            +S+ DD  K       +  TD+ F   A GI++++  LY  FW
Sbjct: 590 KSSLQDD--KAYDFNPDIIKTDKVFFTMAMGIVVIIVALYAYFW 631


Lambda     K      H
   0.326    0.141    0.421 

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: 1106
Number of extensions: 50
Number of successful extensions: 6
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: 543
Length of database: 631
Length adjustment: 37
Effective length of query: 506
Effective length of database: 594
Effective search space:   300564
Effective search space used:   300564
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: 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:

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