Alignments for a candidate for iatA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Azospirillum brasilense Sp245

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 AZOBR_RS06950 AZOBR_RS06950 ABC transporter

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__azobra:AZOBR_RS06950
          Length = 520

 Score =  275 bits (704), Expect = 2e-78
 Identities = 179/481 (37%), Positives = 264/481 (54%), Gaps = 16/481 (3%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           L++  ++K FPG  A DQVDLV+  GE+HALLGENGAGKSTL+KI+     ADAG + + 
Sbjct: 13  LELRGITKRFPGCLANDQVDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRIQWN 72

Query: 64  GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQA 123
           G      D P   ++LGI  ++Q F+LF  L+VAEN+ LG +  + G +D   L A    
Sbjct: 73  GHDTHIPD-PAGARRLGIGMVFQHFSLFDTLTVAENISLGLD--QPGPID--ALSARIAE 127

Query: 124 LLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAII 183
           +    GL L+P   V  L+V E+Q VEI + +  + +L+IMDEPT+ L+ +E  RL   +
Sbjct: 128 VSERYGLSLDPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTSVLTPQEATRLFETL 187

Query: 184 AGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVEF 243
             L A   +++Y+SH+L E++A+CD  TV+R GR V S D        +  +M+G  +  
Sbjct: 188 RRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETARSLAEMMIGTELST 247

Query: 244 ERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLAR 303
             R  +   GA  L+V  ++  +    A   L+ VSF  R GEI+G+AG+ G G+ +L  
Sbjct: 248 PERLPQGEAGAAKLQVRHLSTTSDNPFATN-LKDVSFEVRAGEILGIAGVAGNGQAELMA 306

Query: 304 LIFG----ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRN-- 357
            + G     DP +   V ++ +P     PR+    G+  VPE+R  +G   + S+  N  
Sbjct: 307 ALSGEALVPDPAS---VAIEGRPAGHLGPRERRLLGLAFVPEERLGRGAVPELSLSENAL 363

Query: 358 LSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAM 417
           LS  + + L   G     RA R   E       +           LSGGN QK ++GR +
Sbjct: 364 LSGYAREPLVRSGLVHFGRA-RSYAERIIGAFNVVTHGHRAEARSLSGGNLQKFIIGREI 422

Query: 418 ALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFRE 477
              P++L+V +PT G+D GA A +H+ L DLA  G AV+VIS +L E+  +SDRI V   
Sbjct: 423 LQKPRLLVVGQPTWGVDAGAAAAIHRALIDLARAGAAVLVISQDLDELFVLSDRIAVLFH 482

Query: 478 G 478
           G
Sbjct: 483 G 483



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 75/252 (29%), Positives = 111/252 (44%), Gaps = 25/252 (9%)

Query: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316
           L++ G+T   P   A     QV    R GEI  L G  GAG++ L ++I+G     AGR+
Sbjct: 13  LELRGITKRFPGCLAND---QVDLVLRPGEIHALLGENGAGKSTLVKIIYGVLHADAGRI 69

Query: 317 LVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP-----SLKALSALGQ 371
             +     +  P  A + GI +V +       F   ++  N+SL       + ALSA   
Sbjct: 70  QWNGHDTHIPDPAGARRLGIGMVFQ---HFSLFDTLTVAENISLGLDQPGPIDALSARIA 126

Query: 372 WVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTR 431
            V ER    L             D    +  LS G +Q+V + R +   PK+LI+DEPT 
Sbjct: 127 EVSERYGLSL-------------DPRRHVHNLSVGERQRVEIVRCLLQDPKLLIMDEPTS 173

Query: 432 GIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATE 491
            +       + + L  LA  G  ++ IS +L E+ A+ D   V R G +V   D +  T 
Sbjct: 174 VLTPQEATRLFETLRRLAAEGCTILYISHKLEEIRALCDTATVLRGGRVVGSCDPRRETA 233

Query: 492 EGLMAYMATGTD 503
             L A M  GT+
Sbjct: 234 RSL-AEMMIGTE 244



 Score = 67.0 bits (162), Expect = 2e-15
 Identities = 65/237 (27%), Positives = 104/237 (43%), Gaps = 16/237 (6%)

Query: 14  PGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSA-AHAADAGTVTFAGQV---LDP 69
           P    L  V   V  GE+  + G  G G++ L+  LS  A   D  +V   G+    L P
Sbjct: 273 PFATNLKDVSFEVRAGEILGIAGVAGNGQAELMAALSGEALVPDPASVAIEGRPAGHLGP 332

Query: 70  RDAPLRRQQLGIATIYQEF---NLFPELSVAENMYLG---REPR-RLGLVDWSRLRADAQ 122
           R+    R+ LG+A + +E       PELS++EN  L    REP  R GLV + R R+ A+
Sbjct: 333 RE----RRLLGLAFVPEERLGRGAVPELSLSENALLSGYAREPLVRSGLVHFGRARSYAE 388

Query: 123 ALLNDLGLPLNPD-APVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
            ++    +  +   A  R L+    Q   I + +    RL+++ +PT  +       +H 
Sbjct: 389 RIIGAFNVVTHGHRAEARSLSGGNLQKFIIGREILQKPRLLVVGQPTWGVDAGAAAAIHR 448

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238
            +  L     +V+ +S  L E+  + DR  V+  G    S       V ++  LM G
Sbjct: 449 ALIDLARAGAAVLVISQDLDELFVLSDRIAVLFHGHLSESRPTHHTSVEEIGLLMGG 505


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: 640
Number of extensions: 31
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: 520
Length adjustment: 35
Effective length of query: 480
Effective length of database: 485
Effective search space:   232800
Effective search space used:   232800
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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