GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudovibrio axinellae Ad2

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  271 bits (693), Expect = 4e-77
 Identities = 181/523 (34%), Positives = 281/523 (53%), Gaps = 22/523 (4%)

Query: 4   MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 63
           M +T T  PLL+L+NI K F  + A   V L  +AGE+ AL+GENGAGK+TLM IL G Y
Sbjct: 1   MPETETVHPLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHY 60

Query: 64  TADPGGECHIDGQRVQID----GPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR 119
            AD G           +D     PQ+A + G+ +++Q  +LA NL+  ENI LG      
Sbjct: 61  VADEGRVMVRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFA 120

Query: 120 GLVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTT 179
              +R          +   G +      V+ L++ +RQ VEI +A++ +ARILV+DEPT 
Sbjct: 121 RKFSRSKARAKLQELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTA 180

Query: 180 PLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQ 239
            L+  E+D LF  ++ L  +GMAI++ISH+MAE+   +DRV VLR G  V  L  +   +
Sbjct: 181 VLTPQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDR 240

Query: 240 AALVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRR-VKGCSFDLRAGEVLGLAGL 298
             L ++MVG  +     +  G   E  ++       +GR  ++  +  LR GE++GLAG+
Sbjct: 241 HKLAELMVGHAVQ-MAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGV 299

Query: 299 VGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQ 358
            G G++ LA+++ G +  T G V +    GS  L    A     AI +G+A + EDR   
Sbjct: 300 SGNGQSMLAKVLSGLEEPTAGAVTL----GSQPLKANAAA----AIQSGVARIPEDRHHD 351

Query: 359 GLFLDQSVHENINLIVAARDA---LGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGAL 415
           G+    SV EN+ L    + A    GL R N    R+R  EAI    IR +        L
Sbjct: 352 GIVGAMSVEENLVLEEIRKPAYQRFGLLRFNE--IRKRAQEAIKAYDIRCSGPLAVSRLL 409

Query: 416 SGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELP 475
           SGGN QK++L+R L+ +P +++  +P+RG+D+GA ++++R +      G  +L+IS +L 
Sbjct: 410 SGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLD 469

Query: 476 EVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAA 518
           E+  L DR+ V+  G ++    P  S    ++++  +  G +A
Sbjct: 470 ELFQLSDRIAVIHRGHVS---EPMASEELDKKQVGLMMAGHSA 509



 Score = 61.6 bits (148), Expect = 7e-14
 Identities = 61/237 (25%), Positives = 101/237 (42%), Gaps = 10/237 (4%)

Query: 25  GVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQ 84
           G   +  V L+   GE+  L G +G G+S L K+LSG    +P       G +       
Sbjct: 277 GRELIENVNLSLRKGEIIGLAGVSGNGQSMLAKVLSGL--EEPTAGAVTLGSQPLKANAA 334

Query: 85  SARDLGVAVIYQEL---SLAPNLSVAENIYLGR----ALQRRGLVARGDMVRACAPTLAR 137
           +A   GVA I ++     +   +SV EN+ L      A QR GL+   ++ +     +  
Sbjct: 335 AAIQSGVARIPEDRHHDGIVGAMSVEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKA 394

Query: 138 LGADFS-PAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196
                S P A    LS    Q + +AR +  E  I++  +P+  L    T  +   +++ 
Sbjct: 395 YDIRCSGPLAVSRLLSGGNIQKIVLARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEA 454

Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSG 253
           R  G  +L IS  + E+ +L+DR+ V+  G     +    L +  +  MM G    G
Sbjct: 455 RDRGAGVLLISEDLDELFQLSDRIAVIHRGHVSEPMASEELDKKQVGLMMAGHSAKG 511


Lambda     K      H
   0.320    0.136    0.382 

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: 583
Number of extensions: 31
Number of successful extensions: 9
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: 540
Length of database: 515
Length adjustment: 35
Effective length of query: 505
Effective length of database: 480
Effective search space:   242400
Effective search space used:   242400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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