GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Collimonas arenae Ter10

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_061533937.1 CAter10_RS14380 D-xylose ABC transporter ATP-binding protein

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



>NCBI__GCF_001584165.1:WP_061533937.1
          Length = 518

 Score =  379 bits (974), Expect = e-109
 Identities = 219/503 (43%), Positives = 316/503 (62%), Gaps = 17/503 (3%)

Query: 22  YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA--GE 79
           YLLE+  I K F  V AL  + L+VR G  + L GENGAGKSTLMK+++G+Y   +  GE
Sbjct: 4   YLLEMKGIVKQFGAVRALDGIALKVRAGECVGLCGENGAGKSTLMKVLSGVYPHGSWEGE 63

Query: 80  IRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHR 139
           I   G+P+  ++    + AGI +IHQEL L+P +S+AENI++G E       +N+  M+R
Sbjct: 64  ILWDGQPLKAQSIRDTEAAGIVIIHQELMLVPELSVAENIFMGHELTLPGGRMNYPAMYR 123

Query: 140 CTAELLARLRINLDPEEQVG----NLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKE 195
              EL+  L++   PE  V           +Q+VEIAKA++  + +LI+DEP+S++T  E
Sbjct: 124 RADELVRELKM---PEMNVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTTSE 180

Query: 196 VAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISM 255
           +A L  II DLK++G   VYI+HK++EV AI D V+V RDG +I       +N + +I+ 
Sbjct: 181 IAVLLDIIRDLKAKGVACVYISHKLDEVAAICDTVSVIRDGQHIATTPMQELNVEYIIAQ 240

Query: 256 MVGRELSQLFPLRETPIGDLLLTVRDLTLDGV-------FKDVSFDLHAGEILGIAGLMG 308
           MVGRE++ L+P +E  IG+++   R ++   V         D+SF L  GEILG+AGL+G
Sbjct: 241 MVGREMNNLYPKQEHAIGEVVFEARHISCYDVDNPARKKVDDISFSLRKGEILGVAGLVG 300

Query: 309 SGRTNVAETIFGITPS-SSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSV 367
           +GRT +   ++G  P    G++ LDGK V    P  ++  G  ++ EDRK  G+   L+V
Sbjct: 301 AGRTELVSALYGAYPGRQEGEVWLDGKQVDTGSPMKSLRLGLCMVPEDRKRHGIVADLNV 360

Query: 368 LENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLAR 427
            +N+ + VL  ++  G I  +A     +    KLR+KT S    I +LSGGNQQKA+LA+
Sbjct: 361 GQNITLTVLQEFSRFGRIDAEAELQTIQQQIGKLRLKTASPFLPITSLSGGNQQKAVLAK 420

Query: 428 WLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVM 487
            L+  PR+LILDEPTRG+DVGAK EIY+L+  LA +G+A+IM+SSEL EVLG+SDRV+V+
Sbjct: 421 MLLAKPRVLILDEPTRGVDVGAKYEIYKLMFDLAEQGVAIIMVSSELAEVLGVSDRVLVI 480

Query: 488 HEGELMGTLDRSEATQEKVMQLA 510
            EG+L G       TQE V+  A
Sbjct: 481 GEGKLRGDFVNQGLTQETVLAAA 503


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: 600
Number of extensions: 28
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 517
Length of database: 518
Length adjustment: 35
Effective length of query: 482
Effective length of database: 483
Effective search space:   232806
Effective search space used:   232806
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