Alignments for a candidate for iatA in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Collimonas pratensis Ter91

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_061941304.1 CPter91_RS14020 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_001584185.1:WP_061941304.1
          Length = 519

 Score =  357 bits (917), Expect = e-103
 Identities = 200/476 (42%), Positives = 301/476 (63%), Gaps = 4/476 (0%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           L +S + K+F GV AL++V L +  GEVH L+G+NGAGKSTLIK+L+  +  D+G +   
Sbjct: 20  LTLSGICKAFGGVTALNEVALRLYPGEVHTLMGQNGAGKSTLIKVLTGVYTPDSGRILLH 79

Query: 64  GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQA 123
           GQ + PR   L  Q LGI+T+YQE NL P LSVAEN+++GR P++ G +DW  ++  AQ 
Sbjct: 80  GQPVQPRST-LEAQSLGISTVYQEVNLCPNLSVAENIFIGRYPKKYGAIDWKSMQQQAQQ 138

Query: 124 LLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAII 183
           LL++L + ++  AP+    +A QQMV I++A++++A+++I+DEPT++L   EV  L  ++
Sbjct: 139 LLHELHVRIDVAAPLSRYPLAIQQMVAISRALSISAKVLILDEPTSSLDDAEVKLLFEVL 198

Query: 184 AGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVEF 243
             L+A+ +++++V+H L +   + DR TV+R+G+       + +   D+V  MVG     
Sbjct: 199 RKLRAQGMAILFVTHFLEQTYEISDRITVLRNGQLEGEYLASQLSRLDLVNKMVGSQTSS 258

Query: 244 ERRKRRRPPGAVVLKVEGVTPA--APRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
                     A      G T    A  L   G L  +    RGGE++GL GL+G+GRT+ 
Sbjct: 259 SPNLDAADGRAEPQVDSGQTAVLQARGLGRNGILAPLDLDLRGGEVLGLCGLLGSGRTET 318

Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361
           ARL+FGAD   +G + +  K  +  SPRDAI AGI    EDRK++G  L+ S+R N+ L 
Sbjct: 319 ARLLFGADKPDSGTLQIKGKVEKFHSPRDAIAAGIGFCSEDRKKEGAILELSVRENIVL- 377

Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421
           +L+A + L + +  R ++ L   Y + L IK AD ET IG LSGGNQQK LL R +A  P
Sbjct: 378 ALQARAGLLRVIPRRRQQALASDYVKWLGIKTADIETPIGSLSGGNQQKALLARWLATDP 437

Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFRE 477
            +LI+DEPTRGID+ AK E+ + +  L   G+A++ ISSE++EV+ VSDR++V R+
Sbjct: 438 AMLILDEPTRGIDVRAKQEIMEHVIALCRKGMAILFISSEISEVLRVSDRMLVLRD 493



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 64/259 (24%), Positives = 125/259 (48%), Gaps = 11/259 (4%)

Query: 253 GAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIA 312
           GA  L + G+  A   ++A   L +V+     GE+  L G  GAG++ L +++ G     
Sbjct: 16  GAPALTLSGICKAFGGVTA---LNEVALRLYPGEVHTLMGQNGAGKSTLIKVLTGVYTPD 72

Query: 313 AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQW 372
           +GR+L+  +P++ RS  +A   GI  V ++        + S+  N+ +           W
Sbjct: 73  SGRILLHGQPVQPRSTLEAQSLGISTVYQE---VNLCPNLSVAENIFIGRYPKKYGAIDW 129

Query: 373 VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRG 432
              ++ +   +    +L +++ D    + +     QQ V + RA++++ KVLI+DEPT  
Sbjct: 130 ---KSMQQQAQQLLHELHVRI-DVAAPLSRYPLAIQQMVAISRALSISAKVLILDEPTSS 185

Query: 433 IDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEE 492
           +D      + +VL  L   G+A++ ++  L +   +SDRI V R G +  +  A   +  
Sbjct: 186 LDDAEVKLLFEVLRKLRAQGMAILFVTHFLEQTYEISDRITVLRNGQLEGEYLASQLSRL 245

Query: 493 GLMAYMATGTDRVAAPDME 511
            L+  M  G+   ++P+++
Sbjct: 246 DLVNKM-VGSQTSSSPNLD 263


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: 624
Number of extensions: 37
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 515
Length of database: 519
Length adjustment: 35
Effective length of query: 480
Effective length of database: 484
Effective search space:   232320
Effective search space used:   232320
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources