GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Pseudomonas fluorescens FW300-N2C3

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 AO356_28510 AO356_28510 xylose transporter

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28510
          Length = 518

 Score =  332 bits (852), Expect = 2e-95
 Identities = 196/499 (39%), Positives = 306/499 (61%), Gaps = 7/499 (1%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAA--HAADAGTV 60
           LL ++ + K+F GV+AL+ +D+ V  GE   L GENGAGKSTL+K+LSA   H    G +
Sbjct: 5   LLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPHGTWEGEI 64

Query: 61  TFAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLG-LVDWSRLRA 119
            + GQ L  +      +  GI  I+QE  L P+LSVAEN+++G E    G  +++  +  
Sbjct: 65  IWDGQPLKAQSIS-ETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMIH 123

Query: 120 DAQALLNDLGLP-LNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDR 178
            A+AL+ +L +P +N   PV       QQ+VEIAKA+   ARL+I+DEP++AL+  E++ 
Sbjct: 124 RAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEV 183

Query: 179 LHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238
           L  II  LKA+ V+ +Y+SH+L EV A+CD  +V+RDG+ +A+  + D+++  ++  MVG
Sbjct: 184 LLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMTDMDIPKIITQMVG 243

Query: 239 RHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298
           R +           G V+ +   VT           +  +SF  + GEI+G+AGLVGAGR
Sbjct: 244 REMSNLYPTEPHDIGEVIFEARHVTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAGR 303

Query: 299 TDLARLIFGADPIA-AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRN 357
           T+L   +FGA P    G V ++ + +  R+P  +I+AG+ +VPEDRK+QG   D  + +N
Sbjct: 304 TELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQN 363

Query: 358 LSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAM 417
           ++L  L   S L + +D  AE   ++    ++ +K A     I  LSGGNQQK +L + +
Sbjct: 364 ITLAVLDNYSKLTR-IDAEAELGSIDKEIARMHLKTASPFLPITSLSGGNQQKAVLAKML 422

Query: 418 ALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFRE 477
              P+VLI+DEPTRG+D+GAK E+++++  LA  GV+++++SSELAEV+ VSDR++V  +
Sbjct: 423 LTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVIGD 482

Query: 478 GVIVADLDAQTATEEGLMA 496
           G +  D      T+E ++A
Sbjct: 483 GQLRGDFINHELTQEQVLA 501


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: 662
Number of extensions: 39
Number of successful extensions: 11
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: 518
Length adjustment: 35
Effective length of query: 480
Effective length of database: 483
Effective search space:   231840
Effective search space used:   231840
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:

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