GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Rhodobacter johrii JA192

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  290 bits (742), Expect = 8e-83
 Identities = 181/480 (37%), Positives = 269/480 (56%), Gaps = 13/480 (2%)

Query: 13  PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72
           PV+   +V++ FG    L DV   + PGE HAL+G NGAGKST + IL G   P  GEV 
Sbjct: 4   PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVL 63

Query: 73  FSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDAR 132
             G      + R+A    V  ++Q   +   L+V EN+F+ R+  RG  +D +AM+ ++R
Sbjct: 64  LDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAESR 123

Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192
            LL+     V   AR   LSV  RQ+VEIA+AL   AR +I+DEPTA L   E   L  +
Sbjct: 124 RLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQ 183

Query: 193 ISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG-ERG 251
           +  L+  G   L+ SH L EV  I   VTVLRD R +++AP   L  +++ E M G E  
Sbjct: 184 VDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRELS 243

Query: 252 GLAVADAAARGALPADTAVALELKELTGADY-EGVSFTVKRGEVVGLTGATSSGRTSVAE 310
           GL    ++     PA   V LE+  LT   +    SFT++RGEV+G  G   SGRT + E
Sbjct: 244 GLFPPKSS-----PAPEPV-LEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELME 297

Query: 311 AIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIA 370
            I GLR A  G + ++G+ LP   V A+ A G+  + +DR  +GL+L + + EN ++   
Sbjct: 298 GIVGLRPA-TGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLAL 356

Query: 371 RVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSG-LSGGNQQKVVMARALATNPNV 429
              G+  I   A++ A  Q + D    +  G   + +G LSGGNQQK+++A+ +   P V
Sbjct: 357 DRFGRVLIDKAAEERALTQAISDF--DIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRV 414

Query: 430 LVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAE 488
           +++ +PT G+DV +K+ +   + R+  EG++V+VVS EL + +   +RV+VM  GR+A E
Sbjct: 415 VIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGE 474



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 60/226 (26%), Positives = 98/226 (43%), Gaps = 10/226 (4%)

Query: 30  LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRE 89
           + D S  +  GE     G  G+G++ L+  + GLR P TGEVR  G+  P  +   A   
Sbjct: 269 VRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGLR-PATGEVRMEGSPLPHASVSAA--R 325

Query: 90  RVACVY-----QHSTIIRDLSVAENLFINRQPLRGGV-IDWQAMRRDARALLDHWKIDVR 143
               VY     +   ++    + ENL +      G V ID  A  R     +  + I V 
Sbjct: 326 AAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGRVLIDKAAEERALTQAISDFDIRVG 385

Query: 144 EDA-RAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVT 202
           +    AG LS   +Q + +A+ +    R +I+DEPT  +D    ++++  I+ L  EG +
Sbjct: 386 DRGISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRS 445

Query: 203 FLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248
            + +S  L EV  +   V V+   R        A+  E ++    G
Sbjct: 446 VIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEAITEENIVRLAMG 491


Lambda     K      H
   0.318    0.134    0.377 

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: 563
Number of extensions: 31
Number of successful extensions: 8
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: 510
Length of database: 499
Length adjustment: 34
Effective length of query: 476
Effective length of database: 465
Effective search space:   221340
Effective search space used:   221340
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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:

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