GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Alkalihalobacterium alkalinitrilicum DSM 22532

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 WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  284 bits (726), Expect = 6e-81
 Identities = 176/507 (34%), Positives = 278/507 (54%), Gaps = 16/507 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           ++++  + K FPG+ A D V L V  GE+HALLGENGAGKSTL+ +L   +  + G +  
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122
            G+ +   D P    +LGI  ++Q F L  + +V EN+ LG+EP   G ++  +     +
Sbjct: 64  KGKPVKITD-PNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVE 122

Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182
            +    GL ++P A ++ ++V  QQ VEI K +   A ++I DEPTAAL+ +E+  L  I
Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182

Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242
           +  L +   S+I ++H+L E+  +CDR TV+R GR + + D+++     +  +MVGR V 
Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242

Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPR-LSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
           F   K    P   VL+++ +     R ++A   +  +      GEI+G+AG+ G G+T+L
Sbjct: 243 FSVEKDPAQPKDAVLQIKDLVVKDSRDITA---VNDLHLEVHAGEILGVAGVDGNGQTEL 299

Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361
              I G      G + ++ + +   +PR    AG+  +P+DR + G  LD ++  N+ L 
Sbjct: 300 IEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQ 359

Query: 362 SL--KALSALG----QWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415
           +   K  S  G      + ++A  +L+E Y     ++     T    LSGGNQQK ++ R
Sbjct: 360 TYYQKPYSTSGVLNFNEIYKKA-NELIEDY----DVRTPSEHTLARALSGGNQQKAIIAR 414

Query: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475
            +  +P +LI  +PTRG+D+GA   +H  L    D G AV++IS EL EV+ VSDRI V 
Sbjct: 415 EVDRSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVI 474

Query: 476 REGVIVADLDAQTATEEGLMAYMATGT 502
            EG IVA +DA    E  L   MA G+
Sbjct: 475 YEGKIVAIVDADKTNENELGLLMAGGS 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: 557
Number of extensions: 21
Number of successful extensions: 7
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: 509
Length adjustment: 35
Effective length of query: 480
Effective length of database: 474
Effective search space:   227520
Effective search space used:   227520
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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