GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatA in Dinoroseobacter shibae DFL-12

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= TCDB::B8H229
         (515 letters)



>lcl|FitnessBrowser__Dino:3607108 Dshi_0530 ABC transporter related
           (RefSeq)
          Length = 498

 Score =  332 bits (852), Expect = 1e-95
 Identities = 197/501 (39%), Positives = 299/501 (59%), Gaps = 16/501 (3%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           +D+  ++K + GV ALD VD  V  GE   L GENG+GKSTLIKI+S    A AGTV  A
Sbjct: 10  IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69

Query: 64  GQ---VLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENM-YLGREPRRLGLVDWSRLRA 119
           GQ    L+PR +       G+  I+Q+F+LFP LSVAEN+ +  +   R  L  +  +R 
Sbjct: 70  GQEHVTLNPRISAAA----GVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRD 125

Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179
            A+A L+ +G+ ++ DA V  L VA++Q+V I +A+   A+LIIMDEPT AL+ +EV RL
Sbjct: 126 IARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRL 185

Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239
             II  LK   V+VI+VSH+L EV  + ++  V+R+G+ VA G  ++ +   +   M GR
Sbjct: 186 QGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGR 245

Query: 240 HVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299
            V              +++V+G+  A       G    +SF  R GE++G+ GL+G GRT
Sbjct: 246 DVPEVPPSDVAAGAQTLMQVQGLGKA-------GSFSDISFDLRTGEVLGITGLLGCGRT 298

Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359
            +A+ +FG     AG +LVD  P+ L  P+ A  A I  VPEDR  +G FL  SI RN++
Sbjct: 299 SVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVA 358

Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419
           +  L A ++ G ++D          + ++L++K  D E  +  LSGGNQQ+V L R ++ 
Sbjct: 359 VGRLDAHTS-GGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSR 417

Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479
            P+VLI++ P+ G+D+G+KA++H ++ +LA  G+ V+VIS +L E++A   R++V REG 
Sbjct: 418 APRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGR 477

Query: 480 IVADLDAQTATEEGLMAYMAT 500
           I+  L+    TE+ L   +A+
Sbjct: 478 IIDALEGTALTEDDLAHRLAS 498


Lambda     K      H
   0.320    0.136    0.380 

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: 23
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: 515
Length of database: 498
Length adjustment: 34
Effective length of query: 481
Effective length of database: 464
Effective search space:   223184
Effective search space used:   223184
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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