Alignments for a candidate for iatA in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Cereibacter sphaeroides ATCC 17029

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_011841960.1 RSPH17029_RS14655 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_000015985.1:WP_011841960.1
          Length = 499

 Score =  332 bits (850), Expect = 3e-95
 Identities = 202/495 (40%), Positives = 292/495 (58%), Gaps = 15/495 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L + QVS+ F  V+ L  VD  +  GEVHAL+GENGAGKST +KIL+   A  AG V  
Sbjct: 5   VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64

Query: 63  AGQVLDPRDAPLRRQQ--LGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRAD 120
            G+   P   P  R+    GI  I+QEFNL   L+V EN++LGRE +R   ++   ++A+
Sbjct: 65  DGK---PVHFPSSREAEAAGIVMIHQEFNLATPLTVEENIFLGREMKRGPFLNHRAMQAE 121

Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180
           ++ LL  L   ++P A V  L+V  +QMVEIAKA+ L AR++IMDEPTA L+ RE D L 
Sbjct: 122 SRRLLERLHCTVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLL 181

Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240
             +  L+A   S++Y SH+L EV  + DR TV+RDGR V +     +    M   MVGR 
Sbjct: 182 EQVDRLRASGTSILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRE 241

Query: 241 VEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300
           +      +  P    VL+V G+T        PG++R  SF  R GE++G AGLVG+GRT+
Sbjct: 242 LSGLFPPKSPPAPEPVLEVTGLT-------LPGFVRDASFTLRRGEVLGFAGLVGSGRTE 294

Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360
           L   I G  P A G V ++  PL   S   A  AG++ + EDRK++G  L   +  NL+L
Sbjct: 295 LMEGIVGLRP-ATGEVRMEGSPLPRHSVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTL 353

Query: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420
            +L     +   +D+ AE   +        I++ D   + G LSGGNQQK+LL + M   
Sbjct: 354 LALDRFGRV--LIDKGAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAE 411

Query: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480
           P+V+I+DEPTRGID+G K +++  ++ LA  G +V+V+SSEL EV+ +++R+VV   G I
Sbjct: 412 PRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRI 471

Query: 481 VADLDAQTATEEGLM 495
             +++    TEE ++
Sbjct: 472 AGEVEGDAITEENIV 486



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 62/231 (26%), Positives = 111/231 (48%), Gaps = 21/231 (9%)

Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334
           L  V F  R GE+  L G  GAG++   +++ G    +AG VL+D KP+   S R+A  A
Sbjct: 21  LFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLLDGKPVHFPSSREAEAA 80

Query: 335 GIMLVPEDRK-------QQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQ 387
           GI+++ ++         ++  FL   ++R             G +++ RA +       +
Sbjct: 81  GIVMIHQEFNLATPLTVEENIFLGREMKR-------------GPFLNHRAMQAESRRLLE 127

Query: 388 KLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSD 447
           +L   + D    +  LS  N+Q V + +A+ L  +VLI+DEPT  +       + + +  
Sbjct: 128 RLHCTV-DPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQVDR 186

Query: 448 LADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYM 498
           L   G +++  S +L EV  ++DR+ V R+G  V    A+  +E+ +   M
Sbjct: 187 LRASGTSILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETM 237



 Score = 57.8 bits (138), Expect = 9e-13
 Identities = 61/216 (28%), Positives = 98/216 (45%), Gaps = 9/216 (4%)

Query: 29  GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQ-- 86
           GEV    G  G+G++ L++ +     A  G V   G  L PR +    +  G+  + +  
Sbjct: 279 GEVLGFAGLVGSGRTELMEGIVGLRPA-TGEVRMEGSPL-PRHSVSAARAAGLVYLTEDR 336

Query: 87  -EFNLFPELSVAENMYLGREPR--RLGLVDWSRLRADAQALLNDLGLPLNPDAPVRG-LT 142
            E  L     + EN+ L    R  R+ +   +  RA  QA+ +D  + +       G L+
Sbjct: 337 KEKGLLLGKPLGENLTLLALDRFGRVLIDKGAEERALTQAI-SDFDIRVGDRGISAGSLS 395

Query: 143 VAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRLGE 202
              QQ + +AK M    R++I+DEPT  +      +++  IA L A   SVI VS  L E
Sbjct: 396 GGNQQKLLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPE 455

Query: 203 VKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238
           V  + +R  VM  GR     +   +   ++VRL +G
Sbjct: 456 VIGLANRVVVMSAGRIAGEVEGDAITEENIVRLAMG 491


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: 707
Number of extensions: 36
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 515
Length of database: 499
Length adjustment: 34
Effective length of query: 481
Effective length of database: 465
Effective search space:   223665
Effective search space used:   223665
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 10 2024. 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 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