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_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein

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



>NCBI__GCF_001623255.1:WP_068005521.1
          Length = 515

 Score =  259 bits (663), Expect = 1e-73
 Identities = 164/511 (32%), Positives = 281/511 (54%), Gaps = 13/511 (2%)

Query: 15  PQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQ 74
           P+T     LL + NI+K F  +VA  +V L +  G ++AL+GENGAGK+TLM I+ G Y 
Sbjct: 2   PETETVHPLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYV 61

Query: 75  PDAGEIRLR---GKPIVFE--TPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSL 129
            D G + +R   G  +  E   P AA +AGI M+HQ   L  +++  ENI +G E L + 
Sbjct: 62  ADEGRVMVRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFAR 121

Query: 130 HMVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTS 189
                +   +   EL+    + +D + +V  L++ ERQ VEI KA+  D+ IL++DEPT+
Sbjct: 122 KFSRSKARAKLQ-ELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTA 180

Query: 190 AITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNS 249
            +T +E   LF+ +  L ++G  I++I+HKM EV   +D VAV R G  +        + 
Sbjct: 181 VLTPQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDR 240

Query: 250 DSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLD---GVFKDVSFDLHAGEILGIAGL 306
             L  +MVG  + Q+        G+ +L  + ++      + ++V+  L  GEI+G+AG+
Sbjct: 241 HKLAELMVGHAV-QMAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGV 299

Query: 307 MGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLS 366
            G+G++ +A+ + G+   ++G +TL  + ++ ++   AI+ G A + EDR   G+   +S
Sbjct: 300 SGNGQSMLAKVLSGLEEPTAGAVTLGSQPLK-ANAAAAIQSGVARIPEDRHHDGIVGAMS 358

Query: 367 VLENMEMAVL--PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKAL 424
           V EN+ +  +  P Y   G ++   +R   ++  K   ++          LSGGN QK +
Sbjct: 359 VEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIV 418

Query: 425 LARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRV 484
           LAR L   P +++  +P+RG+DVGA A+++R +      G  V++IS +L E+  +SDR+
Sbjct: 419 LARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRI 478

Query: 485 MVMHEGELMGTLDRSEATQEKVMQLASGMTA 515
            V+H G +   +   E  +++V  + +G +A
Sbjct: 479 AVIHRGHVSEPMASEELDKKQVGLMMAGHSA 509


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: 584
Number of extensions: 39
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: 515
Length adjustment: 35
Effective length of query: 482
Effective length of database: 480
Effective search space:   231360
Effective search space used:   231360
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