GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Pseudovibrio axinellae Ad2

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_068000557.1 PsAD2_RS00555 sugar ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>NCBI__GCF_001623255.1:WP_068000557.1
          Length = 522

 Score =  372 bits (955), Expect = e-107
 Identities = 205/495 (41%), Positives = 307/495 (62%), Gaps = 7/495 (1%)

Query: 24  LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83
           L++  + K F GV AL  V   ++ G V AL+GENGAGKSTL+KI++G+Y  D+G I L 
Sbjct: 19  LDVQGVKKYFGGVKALDGVSFSLKQGEVHALVGENGAGKSTLIKILSGVYSFDSGNISLE 78

Query: 84  GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143
                 E+P  A+  GI ++HQE NL+ H+SIAENI I R   N   ++N  EM+R   E
Sbjct: 79  NTSYQPESPQEAKARGIQVVHQEFNLLEHLSIAENISIERLPRNKYGLLNKGEMNRRARE 138

Query: 144 LLARLRI-NLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202
            L  + + ++D    VG+L IA RQ++EIA+A+   S ILI+DEPT+ +TE+E   LF I
Sbjct: 139 ALDAIGLTDIDVRVPVGSLGIAHRQLIEIARALQSKSQILILDEPTATLTERETKRLFKI 198

Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL- 261
           IA +KS+G  +V+++H ++EVFAI D V VFR+G  +   +   M  + ++  MVGR L 
Sbjct: 199 IAAIKSEGVTVVFVSHHLDEVFAICDRVTVFRNGKTVATDKISHMTPEGVVQRMVGRHLE 258

Query: 262 --SQLFPLRET--PIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAET 317
             ++    ++T  P+   +  +R +   G    +S +LH GEI+GIAGL+GSGR+ +   
Sbjct: 259 AGTRQHTDKQTFGPVALQIDAMRTMQNTGD-TGISLNLHYGEIVGIAGLVGSGRSEILRG 317

Query: 318 IFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP 377
           IFGI P  SG +  DG+ V    P  AI+ G   +TEDRK  GL   + +  N  +  + 
Sbjct: 318 IFGIDPIHSGTVYRDGEEVNFKGPQDAIKAGIGFVTEDRKDEGLILDMPIAANTSLVNIH 377

Query: 378 HYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437
             +  G IQ         +   +L++K         +LSGGNQQK +LA+WL  NP++L+
Sbjct: 378 ELSKTGLIQFTEENRQARESGSRLKLKYGKTADPASSLSGGNQQKVVLAKWLACNPKVLL 437

Query: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLD 497
           LDEPTRG+DVGAKAEIY ++  LA EG+A++++SSE+PE++ ++DR++V+ E  + G L 
Sbjct: 438 LDEPTRGVDVGAKAEIYSILKDLAQEGVALLVVSSEMPELMTLADRIVVLAEHAIQGELK 497

Query: 498 RSEATQEKVMQLASG 512
            SE ++E +++LA G
Sbjct: 498 PSEFSEENILKLAYG 512



 Score = 82.4 bits (202), Expect = 4e-20
 Identities = 53/223 (23%), Positives = 113/223 (50%), Gaps = 5/223 (2%)

Query: 42  VQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIA 101
           + L +  G ++ + G  G+G+S +++ I GI    +G +   G+ + F+ P  A KAGI 
Sbjct: 291 ISLNLHYGEIVGIAGLVGSGRSEILRGIFGIDPIHSGTVYRDGEEVNFKGPQDAIKAGIG 350

Query: 102 MIHQELN---LMPHMSIAENI-WIGREQLNSLHMVNHREMHRCTAELLARLRINLDPE-E 156
            + ++     L+  M IA N   +   +L+   ++   E +R   E  +RL++      +
Sbjct: 351 FVTEDRKDEGLILDMPIAANTSLVNIHELSKTGLIQFTEENRQARESGSRLKLKYGKTAD 410

Query: 157 QVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYI 216
              +LS   +Q V +AK ++ +  +L++DEPT  +     A ++SI+ DL  +G  ++ +
Sbjct: 411 PASSLSGGNQQKVVLAKWLACNPKVLLLDEPTRGVDVGAKAEIYSILKDLAQEGVALLVV 470

Query: 217 THKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGR 259
           + +M E+  +AD + V  +    G  +    + ++++ +  G+
Sbjct: 471 SSEMPELMTLADRIVVLAEHAIQGELKPSEFSEENILKLAYGQ 513


Lambda     K      H
   0.320    0.136    0.381 

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: 587
Number of extensions: 25
Number of successful extensions: 7
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: 517
Length of database: 522
Length adjustment: 35
Effective length of query: 482
Effective length of database: 487
Effective search space:   234734
Effective search space used:   234734
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